diff --git a/core.json b/core.json index a2b744f1..e47d77c8 100644 --- a/core.json +++ b/core.json @@ -7,12 +7,12 @@ "val" : "https://creativecommons.org/publicdomain/zero/1.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-02-22" + "val" : "2023-06-28" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : "https://github.com/oborel/obo-relations/wiki/ROCore" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-22/core.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/core.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -38,8 +38,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." - } + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" + }, + "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000006", @@ -51,8 +52,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." - } + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" + }, + "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000016", @@ -77,8 +79,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." - } + "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" + }, + "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", @@ -95,8 +98,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." - } + "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" + }, + "comments" : [ "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000034", diff --git a/core.obo b/core.obo index 5adf5270..d7d7cf5a 100644 --- a/core.obo +++ b/core.obo @@ -1,9 +1,9 @@ format-version: 1.2 -data-version: ro/releases/2023-02-22/core.owl +data-version: ro/releases/2023-06-28/core.owl ontology: ro/core property_value: http://purl.org/dc/elements/1.1/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage "https://github.com/oborel/obo-relations/wiki/ROCore" xsd:anyURI -property_value: owl:versionInfo "2023-02-22" xsd:string +property_value: owl:versionInfo "2023-06-28" xsd:string [Term] id: BFO:0000002 @@ -19,7 +19,8 @@ def: "An entity that has temporal parts and that happens, unfolds or develops th [Term] id: BFO:0000004 name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] +comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant @@ -32,7 +33,8 @@ is_a: BFO:0000141 ! immaterial entity [Term] id: BFO:0000015 name: process -def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] +comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent [Term] @@ -56,7 +58,8 @@ is_a: BFO:0000020 ! specifically dependent continuant [Term] id: BFO:0000020 name: specifically dependent continuant -def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] +comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant @@ -69,7 +72,8 @@ is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000031 name: generically dependent continuant -def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] +comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. is_a: BFO:0000002 ! continuant [Term] diff --git a/core.owl b/core.owl index a5d262b3..fde746bf 100644 --- a/core.owl +++ b/core.owl @@ -13,9 +13,9 @@ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/"> - + - 2023-02-22 + 2023-06-28 https://github.com/oborel/obo-relations/wiki/ROCore @@ -682,7 +682,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -701,7 +702,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -742,7 +744,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -762,7 +765,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant diff --git a/ro-base.json b/ro-base.json index 0f9a8c13..ceb40ecc 100644 --- a/ro-base.json +++ b/ro-base.json @@ -3,25 +3,25 @@ "id" : "http://purl.obolibrary.org/obo/ro/ro-base.json", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/description", - "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." - }, { - "pred" : "http://purl.org/dc/elements/1.1/title", - "val" : "OBO Relations Ontology" - }, { "pred" : "http://purl.org/dc/elements/1.1/type", "val" : "http://purl.obolibrary.org/obo/IAO_8000001" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/publicdomain/zero/1.0/" + }, { + "pred" : "http://purl.org/dc/terms/title", + "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-02-22" + "val" : "2023-06-28" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-22/ro-base.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/ro-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -47,8 +47,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." - } + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" + }, + "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000006", @@ -60,8 +61,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." - } + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" + }, + "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000016", @@ -86,8 +88,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." - } + "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" + }, + "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", @@ -104,8 +107,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." - } + "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" + }, + "comments" : [ "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000034", @@ -186,6 +190,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -357,6 +364,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { @@ -380,6 +390,10 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl" : "example of usage", + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "lbl" : "definition", @@ -955,6 +969,9 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" } ] } }, { @@ -1225,7 +1242,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -1242,7 +1259,7 @@ "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -1259,7 +1276,7 @@ "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -1273,7 +1290,7 @@ "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -1287,7 +1304,7 @@ "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -1303,7 +1320,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -1319,7 +1336,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -1335,7 +1352,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -1351,7 +1368,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -1365,7 +1382,7 @@ "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -1378,11 +1395,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1395,11 +1412,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1412,12 +1429,12 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1430,11 +1447,11 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1452,7 +1469,7 @@ "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-05-22T16:43:28Z" @@ -1478,6 +1495,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { @@ -1630,6 +1650,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1656,7 +1679,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", @@ -3404,6 +3427,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "consumes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3424,6 +3450,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "produces" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3793,7 +3822,7 @@ "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3875,7 +3904,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Inverse of 'expressed in'" + "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", @@ -4114,6 +4143,9 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -4131,6 +4163,9 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4396,6 +4431,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4431,6 +4469,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4500,7 +4541,7 @@ "val" : "enables part of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4537,6 +4578,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5397,6 +5441,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5428,6 +5475,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5489,9 +5539,6 @@ "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5503,6 +5550,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5732,7 +5782,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5748,6 +5798,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes activity in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -8018,7 +8071,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { @@ -8661,6 +8714,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8681,6 +8737,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -9124,7 +9183,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { @@ -9142,7 +9201,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { @@ -9546,7 +9605,7 @@ "val" : "2018-01-26T23:49:30Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9564,6 +9623,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:51Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9586,7 +9648,7 @@ "val" : "2018-01-26T23:53:14Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9609,7 +9671,7 @@ "val" : "2018-01-26T23:53:22Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9621,7 +9683,7 @@ "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } @@ -9639,6 +9701,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9655,6 +9720,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9828,6 +9896,27 @@ "val" : "inverse of lays eggs on" } } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009001", "lbl" : "has substance added", @@ -9937,7 +10026,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -10236,7 +10325,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10252,7 +10341,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10268,7 +10357,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10285,7 +10374,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10301,7 +10390,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10317,10 +10406,13 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10333,10 +10425,13 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10349,7 +10444,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10363,7 +10458,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10380,10 +10475,13 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10397,10 +10495,13 @@ "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10413,7 +10514,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10429,7 +10530,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10449,7 +10550,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10465,7 +10566,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10481,7 +10582,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10497,7 +10598,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10513,7 +10614,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10529,7 +10630,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10555,7 +10656,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10571,7 +10672,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10588,7 +10689,7 @@ "comments" : [ "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10604,7 +10705,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -10686,7 +10787,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-7258-9596" } ] } @@ -10772,10 +10873,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" } ] } }, { @@ -10792,10 +10893,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" } ] } }, { @@ -10807,10 +10908,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -10826,10 +10927,10 @@ "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -10848,11 +10949,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" } ] } }, { @@ -10887,6 +10988,38 @@ "val" : "2021-11-08T12:00:00Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017003", + "lbl" : "positively correlated with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between entities in which one increases or decreases as the other does the same." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly correlated with" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017004", + "lbl" : "negatively correlated with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between entities in which one increases as the other decreases." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inversely correlated with" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -10941,7 +11074,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -10960,7 +11093,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -10979,13 +11112,273 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://www.wikidata.org/wiki/Property:P3773" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018030", + "lbl" : "chemical relationship", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018031", + "lbl" : "is direct conjugate base of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0018033" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/643" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018032", + "lbl" : "is direct conjugate acid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0018034" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/643" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018033", + "lbl" : "is deprotonated form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." + }, + "xrefs" : [ { + "val" : "obo:chebi#is_conjugate_base_of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "(E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/643" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018034", + "lbl" : "is protonated form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." + }, + "xrefs" : [ { + "val" : "obo:chebi#is_conjugate_acid_of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "(E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/643" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018035", + "lbl" : "is matched small molecular pair with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification.\n\nWhile this is normally called \"matched molecular pair\" in the cheminformatics literaturel, it is labeled as \"matched small molecular pair\" so as to reduce confusion with peptides and other macromolecules, which are also referenced as \"molecules\" in some contexts.\n\nThis relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A.\n\nThis relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "is MMP with" + }, { + "pred" : "hasExactSynonym", + "val" : "is matched molecular pair with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-02-28T18:53:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018036", + "lbl" : "is tautomer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Two chemicals are tautomers if they can be readily interconverted.\n\nThis commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "is desmotrope of" + } ], + "xrefs" : [ { + "val" : "obo:chebi#is_tautomer_of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-03-18T23:49:31Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/697" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018037", + "lbl" : "is substitutent group from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization." + }, + "xrefs" : [ { + "val" : "obo:chebi#is_substituent_group_from" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-03-18T23:49:31Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/697" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018038", + "lbl" : "has functional parent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. \n\nFor example, the relationship between a salt and a freebased compound is a \"has functional parent\" relationship." + }, + "xrefs" : [ { + "val" : "obo:chebi#has_functional_parent" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-03-18T23:49:31Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/697" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018039", + "lbl" : "is enantiomer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center.\n\nA chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers)." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "is optical isomer of" + } ], + "xrefs" : [ { + "val" : "obo:chebi#is_enantiomer_of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-03-18T23:49:31Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/697" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018040", + "lbl" : "has parent hydride", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B." + }, + "xrefs" : [ { + "val" : "obo:chebi#has_parent_hydride" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-03-18T23:49:31Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/697" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0019000", "lbl" : "regulates characteristic", @@ -11035,7 +11428,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" } ] } }, { @@ -12950,7 +13343,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-09-22T11:05:29Z" @@ -12966,7 +13359,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-09-22T11:05:18Z" @@ -12982,7 +13375,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-09-22T11:04:12Z" @@ -12998,7 +13391,7 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-09-22T11:05:45Z" @@ -15266,6 +15659,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009005", "pred" : "subPropertyOf", @@ -15490,6 +15887,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0016004", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002244" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0017003", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002610" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0017004", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002610" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0018001", "pred" : "subPropertyOf", @@ -15510,6 +15915,46 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0018029", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002449" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018031", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018033" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018032", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018034" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018033", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018030" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018034", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018030" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018035", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018030" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018036", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018030" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018037", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018030" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018038", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018030" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018039", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018030" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018040", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018030" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0019000", "pred" : "subPropertyOf", @@ -16282,6 +16727,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0018002", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0018003" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018031", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018032" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0018033", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0018034" } ], "domainRangeAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -16407,12 +16860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002004", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002009", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] @@ -16439,24 +16892,24 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - 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"domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002134", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -16482,8 +16935,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -16499,7 +16952,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -16518,7 +16971,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -16539,12 +16992,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - 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"domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -16679,12 +17132,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -16724,7 +17177,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -16742,12 +17195,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009001", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -16763,7 +17220,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009004", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -16861,13 +17318,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002200", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -16891,13 +17348,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ], "propertyChainAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", diff --git a/ro-base.obo b/ro-base.obo index 3ba11b3f..8dc953e6 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: ro/releases/2023-02-22/ro-base.owl +data-version: ro/releases/2023-06-28/ro-base.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -7,12 +7,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: ro/ro-base -property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 +property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ +property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-02-22" xsd:string +property_value: owl:versionInfo "2023-06-28" xsd:string [Term] id: BFO:0000002 @@ -33,7 +33,8 @@ relationship: RO:HOM0000000 BFO:0000003 {all_only="true"} ! occurrent [Term] id: BFO:0000004 name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] +comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant @@ -47,7 +48,8 @@ is_a: BFO:0000141 ! immaterial entity [Term] id: BFO:0000015 name: process -def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] +comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process @@ -74,7 +76,8 @@ relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 name: specifically dependent continuant -def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] +comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant @@ -88,7 +91,8 @@ is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000031 name: generically dependent continuant -def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] +comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. is_a: BFO:0000002 ! continuant relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant @@ -194,6 +198,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -298,6 +303,7 @@ property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 @@ -613,6 +619,7 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true @@ -671,8 +678,8 @@ id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: RO:0001018 ! contained in [Typedef] @@ -680,8 +687,8 @@ id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: CARO:0000003 -range: CARO:0001001 +domain: UBERON:0000061 +range: UBERON:0000122 inverse_of: RO:0002134 ! innervates [Typedef] @@ -753,7 +760,7 @@ name: has regulatory component activity def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] is_a: RO:0002017 ! has component activity is_a: RO:0002334 ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -763,7 +770,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002335 ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -773,7 +780,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -782,7 +789,7 @@ name: has necessary component activity comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. is_a: RO:0002017 ! has component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -790,7 +797,7 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -800,7 +807,7 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002180 ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -808,7 +815,7 @@ id: RO:0002019 name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] is_a: RO:0002233 ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -816,7 +823,7 @@ id: RO:0002020 name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] is_a: RO:0002313 ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] @@ -824,54 +831,54 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] id: RO:0002026 name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: RO:0002323 ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -886,10 +893,12 @@ is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002082 name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: RO:0002081 ! before or simultaneous with @@ -994,6 +1003,7 @@ subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: RO:0002091 ! starts during is_a: RO:0002093 ! ends during @@ -1011,12 +1021,12 @@ is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002100 name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -1032,7 +1042,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: RO:0002131 ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection @@ -1074,8 +1084,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: BFO:0000051 ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -1167,7 +1177,7 @@ id: RO:0002111 name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string -domain: CARO:0000003 +domain: UBERON:0000061 range: BFO:0000040 ! material entity [Typedef] @@ -1285,7 +1295,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: RO:0002131 ! overlaps [Typedef] @@ -1296,7 +1306,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 transitive_over: BFO:0000050 ! part of expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] @@ -1392,7 +1402,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -range: CARO:0001010 +range: OBI:0100026 holds_over_chain: BFO:0000050 RO:0002162 holds_over_chain: BFO:0000051 RO:0002162 holds_over_chain: RO:0002202 RO:0002162 @@ -1446,8 +1456,8 @@ id: RO:0002177 name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1565,7 +1575,7 @@ property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant -range: CARO:0000006 +range: UBERON:0000465 is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of @@ -1819,7 +1829,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by @@ -1897,6 +1907,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: RO:0002224 RO:0002233 is_a: RO:0000057 ! has participant @@ -1913,6 +1924,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: RO:0002230 RO:0002234 is_a: RO:0000057 ! has participant inverse_of: RO:0002353 ! output of @@ -2036,8 +2048,8 @@ def: "x has developmental contribution from y iff x has some part z such that z property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -2066,8 +2078,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002257 ! developmentally induces @@ -2129,7 +2141,7 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -2173,7 +2185,7 @@ inverse_of: RO:0002293 ! ubiquitously expresses [Typedef] id: RO:0002292 name: expresses -def: "Inverse of 'expressed in'" [] +def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to @@ -2196,7 +2208,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: RO:0002324 ! developmentally related to [Typedef] @@ -2295,7 +2307,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: RO:0002321 ! ecologically related to @@ -2308,6 +2320,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -2319,6 +2332,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -2375,7 +2389,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2442,6 +2456,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: RO:0002216 ! capable of part of is_a: RO:0002329 ! part of structure that is capable of @@ -2458,6 +2473,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -2495,7 +2511,7 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -2519,6 +2535,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to @@ -2748,7 +2765,7 @@ def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -2759,7 +2776,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -2896,8 +2913,8 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: RO:0002324 ! developmentally related to [Typedef] @@ -3004,6 +3021,7 @@ def: "p indirectly positively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 @@ -3026,6 +3044,7 @@ def: "p indirectly negatively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true @@ -3065,11 +3084,11 @@ is_a: RO:0002411 ! causally upstream of id: RO:0002413 name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI holds_over_chain: RO:0002402 RO:0002400 is_a: RO:0002412 ! immediately causally upstream of is_a: RO:0002414 ! transitively provides input for @@ -3174,11 +3193,12 @@ is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -4097,8 +4117,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true @@ -4227,8 +4247,8 @@ name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: RO:0002328 ! functionally related to [Typedef] @@ -4268,7 +4288,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -4298,8 +4318,8 @@ name: participates in a biotic-biotic interaction with subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: RO:0002437 ! biotically interacts with [Typedef] @@ -4308,8 +4328,8 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: BFO:0000050 ! part of [Typedef] @@ -4568,6 +4588,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates @@ -4581,6 +4602,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -4855,7 +4877,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: RO:0004008 name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002234 ! has output is_a: RO:0004007 ! has primary input or output @@ -4865,7 +4887,7 @@ creation_date: 2018-12-13T11:26:32Z [Typedef] id: RO:0004009 name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002233 ! has input is_a: RO:0004007 ! has primary input or output @@ -4967,7 +4989,7 @@ id: RO:0004020 name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -5020,7 +5042,7 @@ id: RO:0004025 name: disease causes dysfunction of property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: https://orcid.org/0000-0002-6601-2165 @@ -5072,7 +5094,7 @@ creation_date: 2017-12-26T19:50:53Z id: RO:0004030 name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] -range: CARO:0000003 +range: UBERON:0000061 is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -5091,7 +5113,7 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -5102,6 +5124,7 @@ id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -5113,7 +5136,7 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect @@ -5126,7 +5149,7 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect @@ -5137,6 +5160,7 @@ creation_date: 2018-01-26T23:53:22Z id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -5145,6 +5169,7 @@ creation_date: 2018-03-13T23:55:05Z id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -5209,16 +5234,16 @@ is_a: RO:0002445 ! parasitized by id: RO:0008505 name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0008506 name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: RO:0002321 ! ecologically related to @@ -5235,6 +5260,19 @@ name: has eggs laid on by def: "inverse of lays eggs on" [] is_a: RO:0002619 ! visited by +[Typedef] +id: RO:0008509 +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: RO:0002303 ! has habitat + [Typedef] id: RO:0009001 name: has substance added @@ -5274,7 +5312,7 @@ property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity -range: CARO:0001010 +range: OBI:0100026 [Typedef] id: RO:0009005 @@ -5289,7 +5327,7 @@ is_a: RO:0009001 ! has substance added id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 @@ -5466,7 +5504,7 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: RO:0000057 ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -5475,7 +5513,7 @@ name: has small molecule activator def: "a relation between a process and a continuant, in which the process is activated by the small molecule continuant" [] is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -5484,7 +5522,7 @@ name: has small molecule inhibitor def: "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant" [] is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012006 ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -5495,7 +5533,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam is_a: RO:0000057 ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -5503,25 +5541,27 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] id: RO:0012005 name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] id: RO:0012006 name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -5529,7 +5569,7 @@ id: RO:0012007 name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] is_a: RO:0040036 ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -5539,7 +5579,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam is_a: RO:0002592 ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -5548,8 +5588,9 @@ name: constitutively upstream of def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: RO:0002304 ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -5558,8 +5599,9 @@ name: removes input for def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: RO:0002305 ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -5567,7 +5609,7 @@ id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: RO:0002411 ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -5576,7 +5618,7 @@ name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -5586,7 +5628,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -5596,7 +5638,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct is_a: RO:0002110 ! has postsynaptic terminal in is_a: RO:0013001 ! has synaptic IO in region transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -5606,7 +5648,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct is_a: RO:0002113 ! has presynaptic terminal in is_a: RO:0013001 ! has synaptic IO in region transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -5614,7 +5656,7 @@ id: RO:0013004 name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013001 ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -5623,7 +5665,7 @@ name: receives synaptic input throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013002 ! receives synaptic input in region is_a: RO:0013004 ! has synaptic IO throughout -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -5632,7 +5674,7 @@ name: sends synaptic output throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013003 ! sends synaptic output to region is_a: RO:0013004 ! has synaptic IO throughout -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -5645,7 +5687,7 @@ synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 is_a: RO:0002360 ! has dendrite location transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -5654,7 +5696,7 @@ name: receives synaptic input from neuron def: "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." [] is_a: RO:0002103 ! synapsed by inverse_of: RO:0013009 ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -5663,7 +5705,7 @@ name: sends synaptic output to cell def: "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." [] comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. is_a: RO:0002120 ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -5671,7 +5713,7 @@ id: RO:0014001 name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] is_a: RO:0004019 ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: RO:0015001 @@ -5705,7 +5747,7 @@ name: has characterizing marker set def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] synonym: "has marker gene combination" EXACT [] synonym: "has marker signature set" EXACT [] -property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000112 "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." xsd:string property_value: IAO:0000112 "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." xsd:string property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string @@ -5762,8 +5804,8 @@ comment: There are frequently two ways to state the same thing: we can say 'sper id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: RO:0002104 ! has plasma membrane part @@ -5772,8 +5814,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: RO:0002104 ! has plasma membrane part @@ -5781,8 +5823,8 @@ is_a: RO:0002104 ! has plasma membrane part [Typedef] id: RO:0016001 name: has phenotype or disease -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -5790,8 +5832,8 @@ property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -5799,10 +5841,10 @@ is_a: RO:0016001 ! has phenotype or disease id: RO:0016004 name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: RO:0002244 ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: RO:0017001 @@ -5817,6 +5859,25 @@ property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-rel holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z +[Typedef] +id: RO:0017003 +name: positively correlated with +def: "A relation between entities in which one increases or decreases as the other does the same." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: IAO:0000118 "directly correlated with" xsd:string +is_reflexive: true +is_symmetric: true +is_a: RO:0002610 ! correlated with + +[Typedef] +id: RO:0017004 +name: negatively correlated with +def: "A relation between entities in which one increases as the other decreases." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: IAO:0000118 "inversely correlated with" xsd:string +is_symmetric: true +is_a: RO:0002610 ! correlated with + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -5843,7 +5904,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003 id: RO:0018027 name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: RO:0002450 ! directly positively regulates activity of @@ -5852,7 +5913,7 @@ is_a: RO:0002450 ! directly positively regulates activity of id: RO:0018028 name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: RO:0002449 ! directly negatively regulates activity of @@ -5861,11 +5922,132 @@ is_a: RO:0002449 ! directly negatively regulates activity of id: RO:0018029 name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: RO:0002449 ! directly negatively regulates activity of +[Typedef] +id: RO:0018030 +name: chemical relationship +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical." xsd:string + +[Typedef] +id: RO:0018031 +name: is direct conjugate base of +def: "A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B." [] +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)" xsd:string +property_value: RO:0002575 RO:0018033 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_a: RO:0018033 ! is deprotonated form of +inverse_of: RO:0018032 ! is direct conjugate acid of + +[Typedef] +id: RO:0018032 +name: is direct conjugate acid of +def: "A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B." [] +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)" xsd:string +property_value: RO:0002575 RO:0018034 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_a: RO:0018034 ! is protonated form of + +[Typedef] +id: RO:0018033 +name: is deprotonated form of +def: "A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." [] +xref: obo:chebi#is_conjugate_base_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "(E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons." xsd:string +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_transitive: true +is_a: RO:0018030 ! chemical relationship +inverse_of: RO:0018034 ! is protonated form of + +[Typedef] +id: RO:0018034 +name: is protonated form of +def: "A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." [] +xref: obo:chebi#is_conjugate_acid_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "(E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons." xsd:string +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_transitive: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018035 +name: is matched small molecular pair with +def: "A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification.\n\nWhile this is normally called \"matched molecular pair\" in the cheminformatics literaturel, it is labeled as \"matched small molecular pair\" so as to reduce confusion with peptides and other macromolecules, which are also referenced as \"molecules\" in some contexts.\n\nThis relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A.\n\nThis relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C." [] {http://purl.org/dc/terms/source="https://doi.org/10.1021/jm200452d", http://purl.org/dc/terms/source="https://doi.org/10.1002/ddr.21045", http://purl.org/dc/terms/source="https://en.wikipedia.org/wiki/Matched_molecular_pair_analysis"} +synonym: "is matched molecular pair with" EXACT [] +synonym: "is MMP with" EXACT [] +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-02-28T18:53:32Z" xsd:dateTime +property_value: IAO:0000112 "phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol." xsd:string +is_symmetric: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018036 +name: is tautomer of +def: "Two chemicals are tautomers if they can be readily interconverted.\n\nThis commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms." [] +synonym: "is desmotrope of" EXACT [] +xref: obo:chebi#is_tautomer_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38707", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38709"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_symmetric: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018037 +name: is substitutent group from +def: "Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization." [] +xref: obo:chebi#is_substituent_group_from +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:30795", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:58957"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018038 +name: has functional parent +def: "Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. \n\nFor example, the relationship between a salt and a freebased compound is a \"has functional parent\" relationship." [] +xref: obo:chebi#has_functional_parent +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50851", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50854"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018039 +name: is enantiomer of +def: "Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center.\n\nA chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers)." [] +synonym: "is optical isomer of" EXACT [] +xref: obo:chebi#is_enantiomer_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:31472"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_symmetric: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018040 +name: has parent hydride +def: "Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B." [] +xref: obo:chebi#has_parent_hydride +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:39106", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:52083"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_a: RO:0018030 ! chemical relationship + [Typedef] id: RO:0019000 name: regulates characteristic @@ -5898,7 +6080,7 @@ id: RO:0019501 name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] is_a: RO:0003304 ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: RO:0040035 diff --git a/ro-base.owl b/ro-base.owl index 742edd48..578d6094 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -18,12 +18,12 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - OBO Relations Ontology + + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - 2023-02-22 + OBO Relations Ontology + 2023-06-28 https://github.com/oborel/obo-relations/ @@ -48,7 +48,9 @@ - + + example of usage + @@ -801,7 +803,7 @@ Where we have an annotation assertion true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - + nominally disjoint with @@ -860,7 +862,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:29Z valid_for_go_annotation_extension @@ -872,7 +874,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:18Z valid_for_go_gp2term @@ -884,7 +886,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:04:12Z valid_for_go_ontology @@ -896,7 +898,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:45Z valid_for_gocam @@ -915,30 +917,12 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - @@ -951,12 +935,6 @@ Where we have an annotation assertion - - - - - - @@ -981,6 +959,12 @@ Where we have an annotation assertion + + + + + + @@ -1149,6 +1133,12 @@ Where we have an annotation assertion + + + + + + @@ -1199,6 +1189,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -1357,6 +1348,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in + https://wiki.geneontology.org/Occurs_in @@ -1820,6 +1812,7 @@ range: spatial region or site (immaterial continuant) http://www.obofoundry.org/ro/#OBO_REL:located_in located in + https://wiki.geneontology.org/Located_in @@ -1904,8 +1897,8 @@ range: spatial region or site (immaterial continuant) - - + + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). tracheates @@ -1917,8 +1910,8 @@ range: spatial region or site (immaterial continuant) - - + + http://www.ncbi.nlm.nih.gov/pubmed/22402613 innervated_by @@ -2072,7 +2065,7 @@ AND t has_input y A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z has regulatory component activity @@ -2085,7 +2078,7 @@ AND t has_input y A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -2099,7 +2092,7 @@ AND t has_input y A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -2112,7 +2105,7 @@ AND t has_input y - dos + 2017-05-24T09:36:08Z A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. has necessary component activity @@ -2124,7 +2117,7 @@ AND t has_input y - dos + 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -2139,7 +2132,7 @@ AND t has_input y w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z has component process @@ -2151,7 +2144,7 @@ AND t has_input y A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z has ligand @@ -2163,7 +2156,7 @@ AND t has_input y Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z transports @@ -2175,7 +2168,7 @@ AND t has_input y A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z occurs across @@ -2187,7 +2180,7 @@ AND t has_input y - dos + 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -2196,7 +2189,7 @@ AND t has_input y Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -2207,7 +2200,7 @@ AND t has_input y Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z directly negatively regulated by @@ -2215,7 +2208,7 @@ AND t has_input y Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -2226,7 +2219,7 @@ AND t has_input y Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z directly positively regulated by @@ -2234,7 +2227,7 @@ AND t has_input y Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -2245,7 +2238,7 @@ AND t has_input y A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -2254,7 +2247,7 @@ AND t has_input y A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -2273,7 +2266,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z in register with @@ -2288,7 +2281,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -2310,7 +2303,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland @@ -2473,6 +2468,7 @@ Examples include: the relationship between two channels collected simultaneously X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -2496,13 +2492,13 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -2518,7 +2514,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -2607,8 +2603,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -2739,7 +2735,7 @@ Examples include: the relationship between two channels collected simultaneously - + has neurotransmitter @@ -2943,7 +2939,7 @@ N1 SubclassOf ( - + @@ -2992,7 +2988,7 @@ N1 SubclassOf ( - + @@ -3133,7 +3129,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3262,8 +3258,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + @@ -3333,8 +3329,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3470,7 +3466,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3492,16 +3488,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - + @@ -3868,7 +3864,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3995,6 +3991,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has input + https://wiki.geneontology.org/Has_input @@ -4017,6 +4014,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has output + https://wiki.geneontology.org/Has_output @@ -4200,8 +4198,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + @@ -4238,8 +4236,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -4346,7 +4344,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -4412,7 +4410,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - Inverse of 'expressed in' + y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. expresses @@ -4437,7 +4435,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -4566,7 +4564,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -4594,6 +4592,7 @@ where holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -4609,6 +4608,7 @@ where causally upstream of, negative effect + @@ -4692,7 +4692,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -4805,6 +4805,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to + https://wiki.geneontology.org/Contributes_to @@ -4833,6 +4834,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables + https://wiki.geneontology.org/Enables @@ -4904,7 +4906,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -4934,6 +4936,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled by + https://wiki.geneontology.org/Enabled_by @@ -5265,7 +5268,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -5275,7 +5278,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -5286,7 +5289,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -5296,7 +5299,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -5493,8 +5496,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -5679,6 +5682,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5717,6 +5721,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5791,12 +5796,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for directly provides input for (process to process) provides input for + https://wiki.geneontology.org/Provides_input_for @@ -5980,6 +5985,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different enables activity in is active in + https://wiki.geneontology.org/Is_active_in @@ -5994,8 +6000,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -7477,8 +7483,8 @@ the a supports either the existence of b, or the truth value of b. - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -7489,7 +7495,7 @@ the a supports either the existence of b, or the truth value of b. - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -7681,8 +7687,8 @@ the a supports either the existence of b, or the truth value of b. - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -7741,7 +7747,7 @@ the a supports either the existence of b, or the truth value of b. x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + lumen of @@ -7780,8 +7786,8 @@ the a supports either the existence of b, or the truth value of b. - - + + participates in a biotic-biotic interaction with @@ -7794,8 +7800,8 @@ the a supports either the existence of b, or the truth value of b. - - + + inverse of has skeleton @@ -8217,6 +8223,7 @@ the a supports either the existence of b, or the truth value of b. directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -8234,6 +8241,7 @@ the a supports either the existence of b, or the truth value of b. directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -8679,7 +8687,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -8703,7 +8711,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -8846,7 +8854,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -8934,7 +8942,7 @@ Environmental exposures include those imposed by natural environments, experimen - + @@ -8956,8 +8964,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -8980,8 +8988,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -9036,7 +9044,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -9074,7 +9082,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -9092,6 +9100,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -9111,7 +9120,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -9131,7 +9140,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -9144,6 +9153,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -9156,6 +9166,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -9252,8 +9263,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for @@ -9265,8 +9276,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. ecologically co-occurs with @@ -9294,6 +9305,23 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -9344,7 +9372,7 @@ Environmental exposures include those imposed by natural environments, experimen - + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -9394,7 +9422,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -9640,7 +9668,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z has small molecule regulator @@ -9653,7 +9681,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z has small molecule activator @@ -9666,7 +9694,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z has small molecule inhibitor @@ -9678,7 +9706,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z @@ -9693,7 +9721,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z is small molecule regulator of @@ -9706,9 +9734,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -9719,9 +9748,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -9731,7 +9761,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z results in adhesion of @@ -9742,7 +9772,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z @@ -9757,11 +9787,12 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -9771,11 +9802,12 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z removes input for + https://wiki.geneontology.org/Removes_input_for @@ -9785,7 +9817,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -9798,7 +9830,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -9814,7 +9846,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -9832,7 +9864,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z receives synaptic input in region @@ -9849,7 +9881,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z sends synaptic output to region @@ -9861,7 +9893,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z has synaptic IO throughout @@ -9874,7 +9906,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z receives synaptic input throughout @@ -9887,7 +9919,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z sends synaptic output throughout @@ -9904,7 +9936,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -9920,7 +9952,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z receives synaptic input from neuron @@ -9932,7 +9964,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. sends synaptic output to cell @@ -9945,7 +9977,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + disease has infectious agent @@ -10003,7 +10035,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. - + has marker gene combination has marker signature set has characterizing marker set @@ -10128,8 +10160,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + has high plasma membrane amount @@ -10148,8 +10180,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + has low plasma membrane amount @@ -10165,8 +10197,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z has phenotype or disease https://github.com/oborel/obo-relations/issues/478 @@ -10178,8 +10210,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -10192,8 +10224,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z has exposure medium @@ -10219,6 +10251,34 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relation between entities in which one increases or decreases as the other does the same. + directly correlated with + + positively correlated with + + + + + + + + + + + A relation between entities in which one increases as the other decreases. + inversely correlated with + + negatively correlated with + + + + @@ -10264,7 +10324,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + is agonist of @@ -10277,7 +10337,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + is inverse agonist of @@ -10290,13 +10350,243 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + is antagonist of + + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical. + + chemical relationship + + + + + + + + + + pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) + A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B. + + + is direct conjugate base of + + + + + + + + + + neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) + A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B. + + + is direct conjugate acid of + + + + + + + + + + + + (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. + A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_base_of + is deprotonated form of + + + + + + + + + + + (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. + A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_acid_of + is protonated form of + + + + + + + + + + + phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol. + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + 2023-02-28T18:53:32Z + is MMP with + is matched molecular pair with + is matched small molecular pair with + + + + + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + + + + + + + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + Two chemicals are tautomers if they can be readily interconverted. + +This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms. + + 2023-03-18T23:49:31Z + obo:chebi#is_tautomer_of + is desmotrope of + is tautomer of + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + + + + + + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. + + 2023-03-18T23:49:31Z + obo:chebi#is_substituent_group_from + is substitutent group from + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + + + + + + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. + +For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship. + + 2023-03-18T23:49:31Z + obo:chebi#has_functional_parent + has functional parent + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + + + + + + + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. + +A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers). + + 2023-03-18T23:49:31Z + obo:chebi#is_enantiomer_of + is optical isomer of + is enantiomer of + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + + + + + + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. + + 2023-03-18T23:49:31Z + obo:chebi#has_parent_hydride + has parent hydride + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + + + + + + @@ -10353,7 +10643,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + confers susceptibility to condition @@ -12020,7 +12310,7 @@ For example, protein A (transcription factor) indirectly increases by expression Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - dos + 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate @@ -12119,7 +12409,8 @@ For example, protein A (transcription factor) indirectly increases by expression - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -12144,7 +12435,8 @@ For example, protein A (transcription factor) indirectly increases by expression - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -12203,7 +12495,8 @@ For example, protein A (transcription factor) indirectly increases by expression - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -12229,7 +12522,8 @@ For example, protein A (transcription factor) indirectly increases by expression - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant @@ -12276,48 +12570,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -12350,6 +12602,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -12407,6 +12665,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -12507,6 +12771,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -12696,13 +12996,13 @@ binary, and takes no temporal argument. - + - + - + @@ -12714,13 +13014,13 @@ binary, and takes no temporal argument. - + - + - + @@ -13396,9 +13696,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13407,9 +13707,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13441,9 +13741,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -13452,9 +13752,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -13486,9 +13786,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -13497,9 +13797,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -13531,9 +13831,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -13542,9 +13842,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -13576,9 +13876,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -13587,9 +13887,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -13621,7 +13921,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13632,7 +13932,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13649,7 +13949,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13659,7 +13959,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13677,7 +13977,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13688,7 +13988,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13705,7 +14005,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13715,7 +14015,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13732,7 +14032,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13743,7 +14043,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13776,9 +14076,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13787,9 +14087,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13820,9 +14120,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13831,9 +14131,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13864,9 +14164,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13875,9 +14175,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13908,9 +14208,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13919,9 +14219,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -13953,8 +14253,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13964,8 +14264,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + diff --git a/ro-full.json b/ro-full.json index 2ddcecaf..98ff4f25 100644 --- a/ro-full.json +++ b/ro-full.json @@ -3,24 +3,90 @@ "id" : "http://purl.obolibrary.org/obo/ro/ro-full.json", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/description", + "pred" : "http://purl.org/dc/terms/description", "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." - }, { - "pred" : "http://purl.org/dc/elements/1.1/title", - "val" : "OBO Relations Ontology" }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/publicdomain/zero/1.0/" + }, { + "pred" : "http://purl.org/dc/terms/title", + "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-02-22" + "val" : "2023-06-28" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-22/ro-full.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/ro-full.json" }, "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "pending final vetting" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000078", + "lbl" : "curation status specification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation status specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000266" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "requires discussion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + } + }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", "type" : "CLASS", @@ -44,8 +110,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." - } + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" + }, + "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000006", @@ -57,8 +124,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." - } + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" + }, + "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000016", @@ -83,8 +151,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." - } + "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" + }, + "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", @@ -101,8 +170,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." - } + "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" + }, + "comments" : [ "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000034", @@ -183,6 +253,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -354,6 +427,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { @@ -377,80 +453,6 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000000", - "lbl" : "anatomical entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", - "xrefs" : [ "CAROC:Brownsville2014" ] - }, - "comments" : [ "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000003", - "lbl" : "connected anatomical structure", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." - }, - "comments" : [ "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000006", - "lbl" : "material anatomical entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An anatomical entity that has mass." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000007", - "lbl" : "immaterial anatomical entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Anatomical entity that has no mass." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0001001", - "lbl" : "neuron projection bundle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0001010", - "lbl" : "organism or virus or viroid", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0010000", - "lbl" : "multicellular anatomical structure", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An anatomical structure that has more than one cell as a part." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "djs93" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -556,6 +558,26 @@ "val" : "2013-09-23T16:04:08Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01000739", + "lbl" : "habitat", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An environmental system which can sustain and allow the growth of an ecological population.", + "xrefs" : [ "EnvO:EnvO" ] + }, + "comments" : [ "A habitat's specificity to an ecological population differentiates it from other environment classes." ], + "xrefs" : [ { + "val" : "EcoLexicon:habitat" + }, { + "val" : "LTER:238" + }, { + "val" : "SWEETRealm:Habitat" + }, { + "val" : "https://en.wikipedia.org/wiki/Habitat" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", "lbl" : "derives from part of", @@ -571,7 +593,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", + "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", "xrefs" : [ "GOC:pdt" ] }, "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], @@ -586,13 +608,15 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.", + "val" : "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.", "xrefs" : [ "GOC:BioGRID", "GOC:jh2", "PMID:9635407" ] }, "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "anaphase-promoting complex activity", - "xrefs" : [ "GOC:dph", "GOC:tb" ] + "pred" : "hasBroadSynonym", + "val" : "E2" + }, { + "pred" : "hasBroadSynonym", + "val" : "E3" }, { "pred" : "hasNarrowSynonym", "val" : "ubiquitin conjugating enzyme activity" @@ -608,12 +632,6 @@ }, { "pred" : "hasNarrowSynonym", "val" : "ubiquitin-conjugating enzyme activity" - }, { - "pred" : "hasRelatedSynonym", - "val" : "E2" - }, { - "pred" : "hasRelatedSynonym", - "val" : "E3" } ], "xrefs" : [ { "val" : "KEGG_REACTION:R03876" @@ -807,6 +825,8 @@ "val" : "Reactome:R-HSA-5691108" }, { "val" : "Reactome:R-HSA-5693108" + }, { + "val" : "Reactome:R-HSA-68712" }, { "val" : "Reactome:R-HSA-69598" }, { @@ -836,220 +856,1630 @@ }, { "val" : "Reactome:R-HSA-9628444" }, { - "val" : "Reactome:R-HSA-9645394" + "val" : "Reactome:R-HSA-9645394" + }, { + "val" : "Reactome:R-HSA-9645414" + }, { + "val" : "Reactome:R-HSA-9688831" + }, { + "val" : "Reactome:R-HSA-9701000" + }, { + "val" : "Reactome:R-HSA-9750946" + }, { + "val" : "Reactome:R-HSA-975118" + }, { + "val" : "Reactome:R-HSA-975147" + }, { + "val" : "Reactome:R-HSA-9758604" + }, { + "val" : "Reactome:R-HSA-9793444" + }, { + "val" : "Reactome:R-HSA-9793485" + }, { + "val" : "Reactome:R-HSA-9793679" + }, { + "val" : "Reactome:R-HSA-9796346" + }, { + "val" : "Reactome:R-HSA-9796387" + }, { + "val" : "Reactome:R-HSA-9796626" + }, { + "val" : "Reactome:R-HSA-9815507" + }, { + "val" : "Reactome:R-HSA-9817362" + }, { + "val" : "Reactome:R-HSA-983140" + }, { + "val" : "Reactome:R-HSA-983153" + }, { + "val" : "Reactome:R-HSA-983156" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0005634", + "lbl" : "nucleus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.", + "xrefs" : [ "GOC:go_curators" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cell nucleus" + }, { + "pred" : "hasNarrowSynonym", + "val" : "horsetail nucleus", + "xrefs" : [ "GOC:al", "GOC:mah", "GOC:vw", "PMID:15030757" ] + } ], + "xrefs" : [ { + "val" : "NIF_Subcellular:sao1702920020" + }, { + "val" : "Wikipedia:Cell_nucleus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0008150", + "lbl" : "biological_process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", + "xrefs" : [ "GOC:pdt" ] + }, + "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "biological process" + }, { + "pred" : "hasExactSynonym", + "val" : "physiological process" + }, { + "pred" : "hasRelatedSynonym", + "val" : "single organism process" + }, { + "pred" : "hasRelatedSynonym", + "val" : "single-organism process" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Biological_process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "jl" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-09-19T15:05:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0016301", + "lbl" : "kinase activity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "comments" : [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "phosphokinase activity" + } ], + "xrefs" : [ { + "val" : "Reactome:R-HSA-6788855" + }, { + "val" : "Reactome:R-HSA-6788867" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0019107", + "lbl" : "myristoyltransferase activity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.", + "xrefs" : [ "GOC:ai" ] + }, + "xrefs" : [ { + "val" : "Reactome:R-HSA-141367" + }, { + "val" : "Reactome:R-HSA-162914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example to be eventually removed" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "lbl" : "data item", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data item" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000030", + "lbl" : "information content entity", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "information content entity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "lbl" : "data about an ontology part", + "meta" : { + "definition" : { + "val" : "Data about an ontology part is a data item about a part of an ontology, for example a term" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data about an ontology part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "failed exploratory term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "lbl" : "editor preferred term", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl" : "example of usage", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example of usage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "lbl" : "in branch", + "meta" : { + "definition" : { + "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "in branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "lbl" : "has curation status", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has curation status" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "lbl" : "term editor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term editor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "lbl" : "alternative label", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like." + }, + "comments" : [ "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "OBO Operations committee" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "lbl" : "definition source", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition source" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "metadata complete" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "organizational term" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ready for release" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "metadata incomplete" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "uncurated" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000224", + "lbl" : "obsolete_core", + "meta" : { + "definition" : { + "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl" : "obsolescence reason specification", + "meta" : { + "definition" : { + "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obsolescence reason specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "placeholder removed" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "terms merged" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term imported" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term split" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has obsolescence reason" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "lbl" : "curator note", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An administrative note of use for a curator but of no use for a user" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curator note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." + }, + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "lbl" : "ontology term requester", + "meta" : { + "definition" : { + "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition." + }, + "comments" : [ "The 'term requester' can credit the person, organization or project who request the ontology term." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology term requester" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "lbl" : "denotator type", + "meta" : { + "definition" : { + "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "universal" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "lbl" : "is denotator type", + "meta" : { + "definition" : { + "val" : "Relates an class defined in an ontology, to the type of it's denotator" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "lbl" : "imported from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "For external terms/classes, the ontology from which the term was imported" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "imported from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "meta" : { + "definition" : { + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "defined class" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "meta" : { + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "named class expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "to be replaced with external ontology term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand expression to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "lbl" : "expand assertion to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand assertion to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "lbl" : "first order logic expression", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "first order logic expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "lbl" : "antisymmetric property", + "meta" : { + "definition" : { + "val" : "Use boolean value xsd:true to indicate that the property is an antisymmetric property" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "antisymmetric property" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part_of antisymmetric property xsd:true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl" : "OBO foundry unique label", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which is unique across the OBO Foundry." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "OBO foundry unique label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBO Foundry " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "lbl" : "has ID digit count", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID digit count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "lbl" : "has ID range allocated to", + "meta" : { + "definition" : { + "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID range allocated" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "lbl" : "has ID policy for", + "meta" : { + "definition" : { + "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID policy for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "lbl" : "has ID prefix", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID prefix" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl" : "elucidation", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "elucidation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Barry Smith" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "lbl" : "has associated axiom(nl)", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(nl)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom associated with a term expressed using natural language" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "lbl" : "has associated axiom(fol)", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(fol)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom expressed in first order logic using CLIF syntax" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "lbl" : "is allocated id range", + "meta" : { + "definition" : { + "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is allocated id range" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "has ontology root term", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ontology root term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Nicolas Matentzoglu" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "lbl" : "may be identical to", + "meta" : { + "definition" : { + "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged." + }, + "comments" : [ "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "may be identical to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "lbl" : "scheduled for obsoletion on or after", + "meta" : { + "definition" : { + "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "scheduled for obsoletion on or after" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall, Jie Zheng" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "lbl" : "has axiom label", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has axiom id" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term replaced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "lbl" : "ontology module", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology file" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "lbl" : "base ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "base ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "lbl" : "editors ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editors ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "lbl" : "main release ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "main release ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "lbl" : "bridge ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bridge ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000005", + "lbl" : "import ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology module that is intended to be imported from another ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "import ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add axioms that indicate this is the output of a module extraction process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "import file" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/extract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000006", + "lbl" : "subset ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology slim" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "subset ontology" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/filter" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000007", + "lbl" : "curation subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation subset ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000008", + "lbl" : "analysis subset ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended for usage in analysis or discovery applications." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "analysis ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000009", + "lbl" : "single layer subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "single layer ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribbon subset" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "lbl" : "exclusion subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "exclusion subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "lbl" : "external import ontology module", + "meta" : { + "definition" : { + "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "external import ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "external import" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "lbl" : "species subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "species subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "taxon subset" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "lbl" : "reasoned ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "reasoned ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "lbl" : "generated ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "generated ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "lbl" : "template generated ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "template generated ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "lbl" : "taxonomic bridge ontology module", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "taxonomic bridge ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "lbl" : "ontology module subsetted by expressivity", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module subsetted by expressivity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "lbl" : "obo basic subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obo basic subset ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "lbl" : "ontology module subsetted by OWL profile", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module subsetted by OWL profile" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "lbl" : "EL++ ontology module", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "EL++ ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0100026", + "lbl" : "organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "animal" }, { - "val" : "Reactome:R-HSA-9645414" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "fungus" }, { - "val" : "Reactome:R-HSA-9688831" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "plant" }, { - "val" : "Reactome:R-HSA-9701000" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "virus" }, { - "val" : "Reactome:R-HSA-975118" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { - "val" : "Reactome:R-HSA-975147" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" }, { - "val" : "Reactome:R-HSA-983140" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." }, { - "val" : "Reactome:R-HSA-983153" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP: OBI Biomaterial Branch" }, { - "val" : "Reactome:R-HSA-983156" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "WEB: http://en.wikipedia.org/wiki/Organism" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005634", - "lbl" : "nucleus", + "id" : "http://purl.obolibrary.org/obo/OGMS_0000031", + "lbl" : "disease", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cell nucleus" - }, { - "pred" : "hasNarrowSynonym", - "val" : "horsetail nucleus", - "xrefs" : [ "GOC:al", "GOC:mah", "GOC:vw", "PMID:15030757" ] - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao1702920020" - }, { - "val" : "Wikipedia:Cell_nucleus" - } ] + "val" : "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." + } } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0008150", - "lbl" : "biological_process", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", "meta" : { "definition" : { - "val" : "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", - "xrefs" : [ "GOC:pdt" ] + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "biological process" - }, { - "pred" : "hasExactSynonym", - "val" : "physiological process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single organism process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism process" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Biological_process" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-09-19T15:05:24Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016301", - "lbl" : "kinase activity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0001001", + "lbl" : "logical characteristic of object property", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", - "xrefs" : [ "ISBN:0198506732" ] + "val" : "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL." }, - "comments" : [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "phosphokinase activity" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-6788855" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBO Operations call" }, { - "val" : "Reactome:R-HSA-6788867" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0019107", - "lbl" : "myristoyltransferase activity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.", - "xrefs" : [ "GOC:ai" ] + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "xrefs" : [ { - "val" : "Reactome:R-HSA-141367" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : \n PREFIX : Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." [GOC:BioGRID, GOC:jh2, PMID:9635407] -synonym: "anaphase-promoting complex activity" NARROW [GOC:dph, GOC:tb] -synonym: "E2" RELATED [] -synonym: "E3" RELATED [] +def: "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." [GOC:BioGRID, GOC:jh2, PMID:9635407] +synonym: "E2" BROAD [] +synonym: "E3" BROAD [] synonym: "ubiquitin conjugating enzyme activity" NARROW [] synonym: "ubiquitin ligase activity" NARROW [] synonym: "ubiquitin protein ligase activity" NARROW [] @@ -327,6 +295,7 @@ xref: Reactome:R-HSA-5675470 "BIRC2/3 (cIAP1/2) is autoubiquitinated" xref: Reactome:R-HSA-5684250 "SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2" xref: Reactome:R-HSA-5691108 "SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2" xref: Reactome:R-HSA-5693108 "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains" +xref: Reactome:R-HSA-68712 "The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1" xref: Reactome:R-HSA-69598 "Ubiquitination of phosphorylated Cdc25A" xref: Reactome:R-HSA-741386 "RIP2 induces K63-linked ubiquitination of NEMO" xref: Reactome:R-HSA-75824 "Ubiquitination of Cyclin D1" @@ -337,7 +306,7 @@ xref: Reactome:R-HSA-9013069 "Ubiquitination of DLL/JAG ligands upon binding to xref: Reactome:R-HSA-9013974 "Auto-ubiquitination of TRAF3 within activated TLR3 complex" xref: Reactome:R-HSA-9014342 "K63-linked ubiquitination of RIP1 bound to the activated TLR complex" xref: Reactome:R-HSA-918224 "DDX58 is K63 polyubiquitinated" -xref: Reactome:R-HSA-936412 "RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS" +xref: Reactome:R-HSA-936412 "RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS" xref: Reactome:R-HSA-936942 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2" xref: Reactome:R-HSA-936986 "Activated TRAF6 synthesizes unanchored polyubiquitin chains" xref: Reactome:R-HSA-9628444 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation" @@ -345,8 +314,18 @@ xref: Reactome:R-HSA-9645394 "Activated TRAF6 synthesizes unanchored polyubiquit xref: Reactome:R-HSA-9645414 "Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer" xref: Reactome:R-HSA-9688831 "STUB1 ubiquitinates RIPK3 at K55, K363" xref: Reactome:R-HSA-9701000 "BRCA1:BARD1 heterodimer autoubiquitinates" +xref: Reactome:R-HSA-9750946 "TRAF2,6 ubiquitinates NLRC5" xref: Reactome:R-HSA-975118 "TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex" xref: Reactome:R-HSA-975147 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane" +xref: Reactome:R-HSA-9758604 "Ubiquitination of IKBKG by TRAF6" +xref: Reactome:R-HSA-9793444 "ITCH polyubiquitinates MLKL at K50" +xref: Reactome:R-HSA-9793485 "PRKN polyubiquitinates RIPK3" +xref: Reactome:R-HSA-9793679 "LUBAC ubiquitinates RIPK1 at K627" +xref: Reactome:R-HSA-9796346 "MIB2 ubiquitinates RIPK1 at K377, K604, K634" +xref: Reactome:R-HSA-9796387 "STUB1 ubiquitinates RIPK1 at K571, K604, K627" +xref: Reactome:R-HSA-9796626 "MIB2 ubiquitinates CFLAR" +xref: Reactome:R-HSA-9815507 "MIB2 ubiquitinates CYLD at K338, K530" +xref: Reactome:R-HSA-9817362 "SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex" xref: Reactome:R-HSA-983140 "Transfer of Ub from E2 to substrate and release of E2" xref: Reactome:R-HSA-983153 "E1 mediated ubiquitin activation" xref: Reactome:R-HSA-983156 "Polyubiquitination of substrate" @@ -364,7 +343,7 @@ xref: Wikipedia:Cell_nucleus [Term] id: GO:0008150 name: biological_process -def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] @@ -392,6 +371,39 @@ xref: Reactome:R-HSA-141367 "Myristoylation of tBID by NMT1" xref: Reactome:R-HSA-162914 "Myristoylation of Nef" is_a: GO:0003674 ! molecular_function +[Term] +id: IAO:0000030 +name: information content entity +is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000111 "information content entity" xsd:string + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 "GROUP:OBI:" xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: OBI:0100026 +name: organism +def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000111 "organism" xsd:string +property_value: IAO:0000112 "animal" xsd:string +property_value: IAO:0000112 "fungus" xsd:string +property_value: IAO:0000112 "plant" xsd:string +property_value: IAO:0000112 "virus" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" xsd:string +property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string +property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string +property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string + [Term] id: OGMS:0000031 name: disease @@ -472,6 +484,136 @@ property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in htt property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string +[Term] +id: UBERON:0000061 +name: anatomical structure +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003] +subset: common_anatomy +subset: upper_level +synonym: "biological structure" EXACT [] +synonym: "connected biological structure" EXACT [CARO:0000003] +xref: AAO:0010825 +xref: AEO:0000003 +xref: BILA:0000003 +xref: CARO:0000003 +xref: EHDAA2:0003003 +xref: EMAPA:0 +xref: FBbt:00007001 +xref: FMA:305751 +xref: FMA:67135 +xref: GAID:781 +xref: HAO:0000003 +xref: http://dbpedia.org/ontology/AnatomicalStructure +xref: MA:0003000 +xref: MESH:D000825 +xref: SCTID:362889002 +xref: TAO:0000037 +xref: TGMA:0001823 +xref: VHOG:0001759 +xref: XAO:0003000 +xref: ZFA:0000037 +is_a: UBERON:0000465 ! material anatomical entity +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + +[Term] +id: UBERON:0000122 +name: neuron projection bundle +def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] +synonym: "funiculus" EXACT [] +synonym: "nerve fiber bundle" EXACT [FBbt:00005099] +synonym: "neural fiber bundle" EXACT [] +xref: CARO:0001001 +xref: FBbt:00005099 +xref: NLX:147821 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0000465 +name: material anatomical entity +def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy +subset: upper_level +xref: AAO:0010264 +xref: AEO:0000006 +xref: BILA:0000006 +xref: CARO:0000006 +xref: EHDAA2:0003006 +xref: FBbt:00007016 +xref: FMA:67165 +xref: HAO:0000006 +xref: TAO:0001836 +xref: TGMA:0001826 +xref: VHOG:0001721 +is_a: BFO:0000040 ! material entity +is_a: UBERON:0001062 ! anatomical entity +disjoint_from: UBERON:0000466 ! immaterial anatomical entity +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + +[Term] +id: UBERON:0000466 +name: immaterial anatomical entity +def: "Anatomical entity that has no mass." [http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy +subset: upper_level +synonym: "immaterial physical anatomical entity" EXACT [FMA:67112] +xref: AAO:0010265 +xref: AEO:0000007 +xref: BILA:0000007 +xref: CARO:0000007 +xref: EHDAA2:0003007 +xref: FBbt:00007015 +xref: FMA:67112 +xref: HAO:0000007 +xref: TAO:0001835 +xref: TGMA:0001827 +xref: VHOG:0001727 +is_a: BFO:0000141 ! immaterial entity +is_a: UBERON:0001062 ! anatomical entity +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + +[Term] +id: UBERON:0001062 +name: anatomical entity +def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy +subset: upper_level +xref: AAO:0010841 +xref: AEO:0000000 +xref: BILA:0000000 +xref: BIRNLEX:6 +xref: CARO:0000000 +xref: EHDAA2:0002229 +xref: FBbt:10000000 +xref: FMA:62955 +xref: HAO:0000000 +xref: MA:0000001 +xref: NCIT:C12219 +xref: TAO:0100000 +xref: TGMA:0001822 +xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} +xref: WBbt:0000100 +xref: XAO:0000000 +xref: ZFA:0100000 +is_a: BFO:0000004 ! independent continuant +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + +[Term] +id: UBERON:0010000 +name: multicellular anatomical structure +def: "An anatomical structure that has more than one cell as a part." [CARO:0010000] +subset: common_anatomy +subset: upper_level +synonym: "multicellular structure" EXACT [FBbt:00100313] +xref: CARO:0010000 +xref: FBbt:00100313 +is_a: UBERON:0000061 ! anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + [Term] id: UPHENO:0001001 name: phenotype @@ -504,6 +646,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -608,6 +751,7 @@ property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 @@ -928,6 +1072,7 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true @@ -986,8 +1131,8 @@ id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: RO:0001018 ! contained in [Typedef] @@ -995,8 +1140,8 @@ id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0001001 ! neuron projection bundle +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000122 ! neuron projection bundle inverse_of: RO:0002134 ! innervates [Typedef] @@ -1068,7 +1213,7 @@ name: has regulatory component activity def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] is_a: RO:0002017 ! has component activity is_a: RO:0002334 ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -1078,7 +1223,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002335 ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -1088,7 +1233,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -1097,7 +1242,7 @@ name: has necessary component activity comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. is_a: RO:0002017 ! has component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -1105,7 +1250,7 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1115,7 +1260,7 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002180 ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1123,7 +1268,7 @@ id: RO:0002019 name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] is_a: RO:0002233 ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -1131,7 +1276,7 @@ id: RO:0002020 name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] is_a: RO:0002313 ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] @@ -1139,54 +1284,54 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] id: RO:0002026 name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: RO:0002323 ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -1201,10 +1346,12 @@ is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002082 name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: RO:0002081 ! before or simultaneous with @@ -1309,6 +1456,7 @@ subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: RO:0002091 ! starts during is_a: RO:0002093 ! ends during @@ -1326,12 +1474,12 @@ is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002100 name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron -range: CARO:0000003 ! connected anatomical structure +range: UBERON:0000465 ! material anatomical entity is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -1347,7 +1495,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron -range: CARO:0001001 ! neuron projection bundle +range: UBERON:0000122 ! neuron projection bundle is_a: RO:0002131 ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection @@ -1389,8 +1537,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 ! material anatomical entity -range: CARO:0000006 ! material anatomical entity +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: BFO:0000051 ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -1482,7 +1630,7 @@ id: RO:0002111 name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string -domain: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure range: BFO:0000040 ! material entity [Typedef] @@ -1600,7 +1748,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 ! neuron projection bundle +domain: UBERON:0000122 ! neuron projection bundle is_a: RO:0002131 ! overlaps [Typedef] @@ -1611,7 +1759,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 ! neuron projection bundle +domain: UBERON:0000122 ! neuron projection bundle transitive_over: BFO:0000050 ! part of expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] @@ -1707,7 +1855,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -range: CARO:0001010 ! organism or virus or viroid +range: OBI:0100026 ! organism holds_over_chain: BFO:0000050 RO:0002162 holds_over_chain: BFO:0000051 RO:0002162 holds_over_chain: RO:0002202 RO:0002162 @@ -1761,8 +1909,8 @@ id: RO:0002177 name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1880,7 +2028,7 @@ property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant -range: CARO:0000006 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of @@ -2134,7 +2282,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 ! anatomical entity +domain: UBERON:0001062 ! anatomical entity holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by @@ -2212,6 +2360,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: RO:0002224 RO:0002233 is_a: RO:0000057 ! has participant @@ -2228,6 +2377,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: RO:0002230 RO:0002234 is_a: RO:0000057 ! has participant inverse_of: RO:0002353 ! output of @@ -2351,8 +2501,8 @@ def: "x has developmental contribution from y iff x has some part z such that z property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 ! anatomical entity -range: CARO:0000000 ! anatomical entity +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -2381,8 +2531,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 ! material anatomical entity -range: CARO:0000006 ! material anatomical entity +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002257 ! developmentally induces @@ -2444,7 +2594,7 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -2488,7 +2638,7 @@ inverse_of: RO:0002293 ! ubiquitously expresses [Typedef] id: RO:0002292 name: expresses -def: "Inverse of 'expressed in'" [] +def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to @@ -2511,7 +2661,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process -range: CARO:0000000 ! anatomical entity +range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] @@ -2610,7 +2760,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 ! organism or virus or viroid +domain: OBI:0100026 ! organism range: ENVO:01000254 ! environmental system is_a: RO:0002321 ! ecologically related to @@ -2623,6 +2773,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -2634,6 +2785,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -2690,7 +2842,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 ! connected anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2757,6 +2909,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: RO:0002216 ! capable of part of is_a: RO:0002329 ! part of structure that is capable of @@ -2773,6 +2926,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -2810,7 +2964,7 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -2834,6 +2988,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to @@ -3063,7 +3218,7 @@ def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! connected anatomical structure +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3074,7 +3229,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! connected anatomical structure +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3211,8 +3366,8 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 ! anatomical entity -range: CARO:0000000 ! anatomical entity +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] @@ -3319,6 +3474,7 @@ def: "p indirectly positively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 @@ -3341,6 +3497,7 @@ def: "p indirectly negatively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true @@ -3380,11 +3537,11 @@ is_a: RO:0002411 ! causally upstream of id: RO:0002413 name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI holds_over_chain: RO:0002402 RO:0002400 is_a: RO:0002412 ! immediately causally upstream of is_a: RO:0002414 ! transitively provides input for @@ -3489,11 +3646,12 @@ is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -4412,8 +4570,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true @@ -4542,8 +4700,8 @@ name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: RO:0002328 ! functionally related to [Typedef] @@ -4583,7 +4741,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -4613,8 +4771,8 @@ name: participates in a biotic-biotic interaction with subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 ! organism or virus or viroid -range: CARO:0001010 ! organism or virus or viroid +domain: OBI:0100026 ! organism +range: OBI:0100026 ! organism is_a: RO:0002437 ! biotically interacts with [Typedef] @@ -4623,8 +4781,8 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: BFO:0000050 ! part of [Typedef] @@ -4883,6 +5041,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates @@ -4896,6 +5055,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -5170,7 +5330,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: RO:0004008 name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002234 ! has output is_a: RO:0004007 ! has primary input or output @@ -5180,7 +5340,7 @@ creation_date: 2018-12-13T11:26:32Z [Typedef] id: RO:0004009 name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002233 ! has input is_a: RO:0004007 ! has primary input or output @@ -5282,7 +5442,7 @@ id: RO:0004020 name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -5335,7 +5495,7 @@ id: RO:0004025 name: disease causes dysfunction of property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 ! disease -range: CARO:0000006 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: https://orcid.org/0000-0002-6601-2165 @@ -5387,7 +5547,7 @@ creation_date: 2017-12-26T19:50:53Z id: RO:0004030 name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] -range: CARO:0000003 ! connected anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -5406,7 +5566,7 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -5417,6 +5577,7 @@ id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -5428,7 +5589,7 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect @@ -5441,7 +5602,7 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect @@ -5452,6 +5613,7 @@ creation_date: 2018-01-26T23:53:22Z id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -5460,6 +5622,7 @@ creation_date: 2018-03-13T23:55:05Z id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -5524,16 +5687,16 @@ is_a: RO:0002445 ! parasitized by id: RO:0008505 name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] -domain: CARO:0001010 ! organism or virus or viroid -range: CARO:0001010 ! organism or virus or viroid +domain: OBI:0100026 ! organism +range: OBI:0100026 ! organism is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0008506 name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -domain: CARO:0001010 ! organism or virus or viroid -range: CARO:0001010 ! organism or virus or viroid +domain: OBI:0100026 ! organism +range: OBI:0100026 ! organism is_symmetric: true is_a: RO:0002321 ! ecologically related to @@ -5550,6 +5713,19 @@ name: has eggs laid on by def: "inverse of lays eggs on" [] is_a: RO:0002619 ! visited by +[Typedef] +id: RO:0008509 +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 ! organism +range: ENVO:01000739 ! habitat +is_a: RO:0002303 ! has habitat + [Typedef] id: RO:0009001 name: has substance added @@ -5589,7 +5765,7 @@ property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity -range: CARO:0001010 ! organism or virus or viroid +range: OBI:0100026 ! organism [Typedef] id: RO:0009005 @@ -5604,7 +5780,7 @@ is_a: RO:0009001 ! has substance added id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 @@ -5781,7 +5957,7 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: RO:0000057 ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -5790,7 +5966,7 @@ name: has small molecule activator def: "a relation between a process and a continuant, in which the process is activated by the small molecule continuant" [] is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -5799,7 +5975,7 @@ name: has small molecule inhibitor def: "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant" [] is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012006 ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -5810,7 +5986,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam is_a: RO:0000057 ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -5818,25 +5994,27 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] id: RO:0012005 name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] id: RO:0012006 name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -5844,7 +6022,7 @@ id: RO:0012007 name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] is_a: RO:0040036 ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -5854,7 +6032,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam is_a: RO:0002592 ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -5863,8 +6041,9 @@ name: constitutively upstream of def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: RO:0002304 ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -5873,8 +6052,9 @@ name: removes input for def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: RO:0002305 ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -5882,7 +6062,7 @@ id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: RO:0002411 ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -5891,7 +6071,7 @@ name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -5901,7 +6081,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -5911,7 +6091,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct is_a: RO:0002110 ! has postsynaptic terminal in is_a: RO:0013001 ! has synaptic IO in region transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -5921,7 +6101,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct is_a: RO:0002113 ! has presynaptic terminal in is_a: RO:0013001 ! has synaptic IO in region transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -5929,7 +6109,7 @@ id: RO:0013004 name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013001 ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -5938,7 +6118,7 @@ name: receives synaptic input throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013002 ! receives synaptic input in region is_a: RO:0013004 ! has synaptic IO throughout -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -5947,7 +6127,7 @@ name: sends synaptic output throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013003 ! sends synaptic output to region is_a: RO:0013004 ! has synaptic IO throughout -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -5960,7 +6140,7 @@ synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -5969,7 +6149,7 @@ name: receives synaptic input from neuron def: "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." [] is_a: RO:0002103 ! synapsed by inverse_of: RO:0013009 ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -5978,7 +6158,7 @@ name: sends synaptic output to cell def: "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." [] comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. is_a: RO:0002120 ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -5986,7 +6166,7 @@ id: RO:0014001 name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] is_a: RO:0004019 ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: RO:0015001 @@ -6020,7 +6200,7 @@ name: has characterizing marker set def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] synonym: "has marker gene combination" EXACT [] synonym: "has marker signature set" EXACT [] -property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000112 "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." xsd:string property_value: IAO:0000112 "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." xsd:string property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string @@ -6077,8 +6257,8 @@ comment: There are frequently two ways to state the same thing: we can say 'sper id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -6087,8 +6267,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -6096,8 +6276,8 @@ is_a: RO:0002104 ! has plasma membrane part [Typedef] id: RO:0016001 name: has phenotype or disease -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -6105,8 +6285,8 @@ property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -6114,10 +6294,10 @@ is_a: RO:0016001 ! has phenotype or disease id: RO:0016004 name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: RO:0002244 ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: RO:0017001 @@ -6132,6 +6312,25 @@ property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-rel holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z +[Typedef] +id: RO:0017003 +name: positively correlated with +def: "A relation between entities in which one increases or decreases as the other does the same." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: IAO:0000118 "directly correlated with" xsd:string +is_reflexive: true +is_symmetric: true +is_a: RO:0002610 ! correlated with + +[Typedef] +id: RO:0017004 +name: negatively correlated with +def: "A relation between entities in which one increases as the other decreases." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: IAO:0000118 "inversely correlated with" xsd:string +is_symmetric: true +is_a: RO:0002610 ! correlated with + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -6158,7 +6357,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003 id: RO:0018027 name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: RO:0002450 ! directly positively regulates activity of @@ -6167,7 +6366,7 @@ is_a: RO:0002450 ! directly positively regulates activity of id: RO:0018028 name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: RO:0002449 ! directly negatively regulates activity of @@ -6176,11 +6375,132 @@ is_a: RO:0002449 ! directly negatively regulates activity of id: RO:0018029 name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: RO:0002449 ! directly negatively regulates activity of +[Typedef] +id: RO:0018030 +name: chemical relationship +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical." xsd:string + +[Typedef] +id: RO:0018031 +name: is direct conjugate base of +def: "A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B." [] +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)" xsd:string +property_value: RO:0002575 RO:0018033 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_a: RO:0018033 ! is deprotonated form of +inverse_of: RO:0018032 ! is direct conjugate acid of + +[Typedef] +id: RO:0018032 +name: is direct conjugate acid of +def: "A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B." [] +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)" xsd:string +property_value: RO:0002575 RO:0018034 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_a: RO:0018034 ! is protonated form of + +[Typedef] +id: RO:0018033 +name: is deprotonated form of +def: "A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." [] +xref: obo:chebi#is_conjugate_base_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "(E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons." xsd:string +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_transitive: true +is_a: RO:0018030 ! chemical relationship +inverse_of: RO:0018034 ! is protonated form of + +[Typedef] +id: RO:0018034 +name: is protonated form of +def: "A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." [] +xref: obo:chebi#is_conjugate_acid_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "(E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons." xsd:string +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_transitive: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018035 +name: is matched small molecular pair with +def: "A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification.\n\nWhile this is normally called \"matched molecular pair\" in the cheminformatics literaturel, it is labeled as \"matched small molecular pair\" so as to reduce confusion with peptides and other macromolecules, which are also referenced as \"molecules\" in some contexts.\n\nThis relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A.\n\nThis relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C." [] {http://purl.org/dc/terms/source="https://doi.org/10.1021/jm200452d", http://purl.org/dc/terms/source="https://doi.org/10.1002/ddr.21045", http://purl.org/dc/terms/source="https://en.wikipedia.org/wiki/Matched_molecular_pair_analysis"} +synonym: "is matched molecular pair with" EXACT [] +synonym: "is MMP with" EXACT [] +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-02-28T18:53:32Z" xsd:dateTime +property_value: IAO:0000112 "phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol." xsd:string +is_symmetric: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018036 +name: is tautomer of +def: "Two chemicals are tautomers if they can be readily interconverted.\n\nThis commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms." [] +synonym: "is desmotrope of" EXACT [] +xref: obo:chebi#is_tautomer_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38707", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38709"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_symmetric: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018037 +name: is substitutent group from +def: "Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization." [] +xref: obo:chebi#is_substituent_group_from +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:30795", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:58957"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018038 +name: has functional parent +def: "Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. \n\nFor example, the relationship between a salt and a freebased compound is a \"has functional parent\" relationship." [] +xref: obo:chebi#has_functional_parent +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50851", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50854"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018039 +name: is enantiomer of +def: "Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center.\n\nA chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers)." [] +synonym: "is optical isomer of" EXACT [] +xref: obo:chebi#is_enantiomer_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:31472"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_symmetric: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018040 +name: has parent hydride +def: "Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B." [] +xref: obo:chebi#has_parent_hydride +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:39106", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:52083"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_a: RO:0018030 ! chemical relationship + [Typedef] id: RO:0019000 name: regulates characteristic @@ -6213,7 +6533,7 @@ id: RO:0019501 name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] is_a: RO:0003304 ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: RO:0040035 diff --git a/ro-full.owl b/ro-full.owl index fd8ecb5d..ff2f151d 100644 --- a/ro-full.owl +++ b/ro-full.owl @@ -8,6 +8,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:cito="http://purl.org/spar/cito/" + xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" @@ -20,11 +21,11 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - OBO Relations Ontology + + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - 2023-02-22 + OBO Relations Ontology + 2023-06-28 https://github.com/oborel/obo-relations/ @@ -49,25 +50,72 @@ - + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + editor preferred term + - + + example of usage + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage + example of usage + - + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + has curation status + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition @@ -75,56 +123,138 @@ - + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + editor note + - + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + term editor + - + + alternative label + + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label + - + + definition source + + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source + - + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + - + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from + - + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + - + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + first order logic expression An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + PERSON:Alan Ruttenberg + first order logic expression @@ -133,7 +263,15 @@ + OBO foundry unique label + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label @@ -141,20 +279,36 @@ - + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + elucidation + - + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + + term replaced by + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by @@ -182,6 +336,7 @@ ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + defined by construct @@ -849,7 +1004,7 @@ Where we have an annotation assertion true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - + nominally disjoint with @@ -908,7 +1063,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:29Z valid_for_go_annotation_extension @@ -920,7 +1075,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:18Z valid_for_go_gp2term @@ -932,7 +1087,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:04:12Z valid_for_go_ontology @@ -944,7 +1099,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:45Z valid_for_gocam @@ -963,6 +1118,22 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + @@ -987,18 +1158,36 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + @@ -1023,12 +1212,24 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -1065,12 +1266,24 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -1106,7 +1319,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + @@ -1122,7 +1341,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + @@ -1130,7 +1355,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + @@ -1146,7 +1377,13 @@ Where we have an annotation assertion + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + @@ -1171,6 +1408,30 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + + + + @@ -1209,12 +1470,35 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + - + has neurotransmitter @@ -3012,7 +3302,7 @@ N1 SubclassOf ( - + @@ -3061,7 +3351,7 @@ N1 SubclassOf ( - + @@ -3202,7 +3492,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3331,8 +3621,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + @@ -3402,8 +3692,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3539,7 +3829,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3561,16 +3851,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - + @@ -3937,7 +4227,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -4064,6 +4354,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has input + https://wiki.geneontology.org/Has_input @@ -4086,6 +4377,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has output + https://wiki.geneontology.org/Has_output @@ -4269,8 +4561,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + @@ -4307,8 +4599,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -4415,7 +4707,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -4481,7 +4773,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - Inverse of 'expressed in' + y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. expresses @@ -4506,7 +4798,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -4635,7 +4927,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -4663,6 +4955,7 @@ where holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -4678,6 +4971,7 @@ where causally upstream of, negative effect + @@ -4761,7 +5055,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -4874,6 +5168,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to + https://wiki.geneontology.org/Contributes_to @@ -4902,6 +5197,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables + https://wiki.geneontology.org/Enables @@ -4973,7 +5269,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -5003,6 +5299,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled by + https://wiki.geneontology.org/Enabled_by @@ -5334,7 +5631,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -5344,7 +5641,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -5355,7 +5652,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -5365,7 +5662,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -5562,8 +5859,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -5748,6 +6045,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5786,6 +6084,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5860,12 +6159,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for directly provides input for (process to process) provides input for + https://wiki.geneontology.org/Provides_input_for @@ -6049,6 +6348,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different enables activity in is active in + https://wiki.geneontology.org/Is_active_in @@ -6063,8 +6363,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -7546,8 +7846,8 @@ the a supports either the existence of b, or the truth value of b. - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -7558,7 +7858,7 @@ the a supports either the existence of b, or the truth value of b. - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -7750,8 +8050,8 @@ the a supports either the existence of b, or the truth value of b. - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -7810,7 +8110,7 @@ the a supports either the existence of b, or the truth value of b. x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + lumen of @@ -7849,8 +8149,8 @@ the a supports either the existence of b, or the truth value of b. - - + + participates in a biotic-biotic interaction with @@ -7863,8 +8163,8 @@ the a supports either the existence of b, or the truth value of b. - - + + inverse of has skeleton @@ -8286,6 +8586,7 @@ the a supports either the existence of b, or the truth value of b. directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -8303,6 +8604,7 @@ the a supports either the existence of b, or the truth value of b. directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -8748,7 +9050,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -8772,7 +9074,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -8915,7 +9217,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -9003,7 +9305,7 @@ Environmental exposures include those imposed by natural environments, experimen - + @@ -9025,8 +9327,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -9049,8 +9351,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -9105,7 +9407,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -9143,7 +9445,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -9161,6 +9463,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -9180,7 +9483,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -9200,7 +9503,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -9213,6 +9516,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -9225,6 +9529,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -9321,8 +9626,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for @@ -9334,8 +9639,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. ecologically co-occurs with @@ -9363,6 +9668,23 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -9413,7 +9735,7 @@ Environmental exposures include those imposed by natural environments, experimen - + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -9463,7 +9785,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -9709,7 +10031,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z has small molecule regulator @@ -9722,7 +10044,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z has small molecule activator @@ -9735,7 +10057,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z has small molecule inhibitor @@ -9747,7 +10069,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z @@ -9762,7 +10084,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z is small molecule regulator of @@ -9775,9 +10097,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -9788,9 +10111,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -9800,7 +10124,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z results in adhesion of @@ -9811,7 +10135,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z @@ -9826,11 +10150,12 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -9840,11 +10165,12 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z removes input for + https://wiki.geneontology.org/Removes_input_for @@ -9854,7 +10180,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -9867,7 +10193,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -9883,7 +10209,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -9901,7 +10227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z receives synaptic input in region @@ -9918,7 +10244,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z sends synaptic output to region @@ -9930,7 +10256,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z has synaptic IO throughout @@ -9943,7 +10269,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z receives synaptic input throughout @@ -9956,7 +10282,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z sends synaptic output throughout @@ -9973,7 +10299,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -9989,7 +10315,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z receives synaptic input from neuron @@ -10001,7 +10327,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. sends synaptic output to cell @@ -10014,7 +10340,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + disease has infectious agent @@ -10072,7 +10398,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. - + has marker gene combination has marker signature set has characterizing marker set @@ -10197,8 +10523,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + has high plasma membrane amount @@ -10217,8 +10543,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + has low plasma membrane amount @@ -10234,8 +10560,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z has phenotype or disease https://github.com/oborel/obo-relations/issues/478 @@ -10247,8 +10573,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -10261,8 +10587,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z has exposure medium @@ -10288,6 +10614,34 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relation between entities in which one increases or decreases as the other does the same. + directly correlated with + + positively correlated with + + + + + + + + + + + A relation between entities in which one increases as the other decreases. + inversely correlated with + + negatively correlated with + + + + @@ -10333,7 +10687,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + is agonist of @@ -10346,7 +10700,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + is inverse agonist of @@ -10359,13 +10713,243 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + is antagonist of + + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical. + + chemical relationship + + + + + + + + + + pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) + A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B. + + + is direct conjugate base of + + + + + + + + + + neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) + A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B. + + + is direct conjugate acid of + + + + + + + + + + + + (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. + A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_base_of + is deprotonated form of + + + + + + + + + + + (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. + A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_acid_of + is protonated form of + + + + + + + + + + + phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol. + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + 2023-02-28T18:53:32Z + is MMP with + is matched molecular pair with + is matched small molecular pair with + + + + + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + + + + + + + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + Two chemicals are tautomers if they can be readily interconverted. + +This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms. + + 2023-03-18T23:49:31Z + obo:chebi#is_tautomer_of + is desmotrope of + is tautomer of + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + + + + + + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. + + 2023-03-18T23:49:31Z + obo:chebi#is_substituent_group_from + is substitutent group from + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + + + + + + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. + +For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship. + + 2023-03-18T23:49:31Z + obo:chebi#has_functional_parent + has functional parent + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + + + + + + + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. + +A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers). + + 2023-03-18T23:49:31Z + obo:chebi#is_enantiomer_of + is optical isomer of + is enantiomer of + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + + + + + + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. + + 2023-03-18T23:49:31Z + obo:chebi#has_parent_hydride + has parent hydride + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + + + + + + @@ -10422,7 +11006,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + confers susceptibility to condition @@ -12095,7 +12679,7 @@ For example, protein A (transcription factor) indirectly increases by expression Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - dos + 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate @@ -12194,7 +12778,8 @@ For example, protein A (transcription factor) indirectly increases by expression - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -12219,7 +12804,8 @@ For example, protein A (transcription factor) indirectly increases by expression - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -12278,7 +12864,8 @@ For example, protein A (transcription factor) indirectly increases by expression - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -12304,7 +12891,8 @@ For example, protein A (transcription factor) indirectly increases by expression - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant @@ -12351,140 +12939,41 @@ For example, protein A (transcription factor) indirectly increases by expression - + - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CARO:0000000 - Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. - anatomical entity + + - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CAROC:Brownsville2014 - - + - - - Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. - CARO:0000003 - Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. - connected anatomical structure + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CALOHA:TS-2035 + FBbt:00007002 + FMA:68646 + GO:0005623 + KUPO:0000002 + MESH:D002477 + VHOG:0001533 + WBbt:0004017 + XAO:0003012 + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + cell + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CARO:mah + - - - - - - - - - - - - An anatomical entity that has mass. - CARO:0000006 - material anatomical entity - - - - - - - - - - - - - - - - Anatomical entity that has no mass. - CARO:0000007 - immaterial anatomical entity - - - - - - - - - A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. - CARO:0001001 - neuron projection bundle - - - - - - - - - Material anatomical entity that is a member of an individual species or is a viral or viroid particle. - Melissa Haendel - organism or virus or viroid - - - - - - - - - An anatomical structure that has more than one cell as a part. - djs93 - CARO:0010000 - multicellular anatomical structure - - - - - - - - - - - - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CALOHA:TS-2035 - FBbt:00007002 - FMA:68646 - GO:0005623 - KUPO:0000002 - MESH:D002477 - VHOG:0001533 - WBbt:0004017 - XAO:0003012 - The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). - cell - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CARO:mah - - - - - + @@ -12508,7 +12997,6 @@ For example, protein A (transcription factor) indirectly increases by expression - The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. @@ -12552,10 +13040,31 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + An environmental system which can sustain and allow the growth of an ecological population. + EcoLexicon:habitat + LTER:238 + SWEETRealm:Habitat + https://en.wikipedia.org/wiki/Habitat + A habitat's specificity to an ecological population differentiates it from other environment classes. + habitat + + + + + An environmental system which can sustain and allow the growth of an ecological population. + EnvO:EnvO + + + + - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. @@ -12564,7 +13073,7 @@ For example, protein A (transcription factor) indirectly increases by expression - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GOC:pdt @@ -12580,7 +13089,9 @@ For example, protein A (transcription factor) indirectly increases by expression true - Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + E2 + E3 KEGG_REACTION:R03876 Reactome:R-HSA-1169394 Reactome:R-HSA-1169395 @@ -12677,6 +13188,7 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-5684250 Reactome:R-HSA-5691108 Reactome:R-HSA-5693108 + Reactome:R-HSA-68712 Reactome:R-HSA-69598 Reactome:R-HSA-741386 Reactome:R-HSA-75824 @@ -12695,26 +13207,33 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-9645414 Reactome:R-HSA-9688831 Reactome:R-HSA-9701000 + Reactome:R-HSA-9750946 Reactome:R-HSA-975118 Reactome:R-HSA-975147 + Reactome:R-HSA-9758604 + Reactome:R-HSA-9793444 + Reactome:R-HSA-9793485 + Reactome:R-HSA-9793679 + Reactome:R-HSA-9796346 + Reactome:R-HSA-9796387 + Reactome:R-HSA-9796626 + Reactome:R-HSA-9815507 + Reactome:R-HSA-9817362 Reactome:R-HSA-983140 Reactome:R-HSA-983153 Reactome:R-HSA-983156 - anaphase-promoting complex activity ubiquitin conjugating enzyme activity ubiquitin ligase activity ubiquitin protein ligase activity ubiquitin protein-ligase activity ubiquitin-conjugating enzyme activity - E2 - E3 GO:0004842 ubiquitin-protein transferase activity - Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. GOC:BioGRID GOC:jh2 PMID:9635407 @@ -13289,6 +13808,12 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-5693108 TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains + + + + Reactome:R-HSA-68712 + The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1 + @@ -13353,7 +13878,7 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-936412 - RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS + RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS @@ -13397,6 +13922,12 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-9701000 BRCA1:BARD1 heterodimer autoubiquitinates + + + + Reactome:R-HSA-9750946 + TRAF2,6 ubiquitinates NLRC5 + @@ -13409,6 +13940,60 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-975147 Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane + + + + Reactome:R-HSA-9758604 + Ubiquitination of IKBKG by TRAF6 + + + + + Reactome:R-HSA-9793444 + ITCH polyubiquitinates MLKL at K50 + + + + + Reactome:R-HSA-9793485 + PRKN polyubiquitinates RIPK3 + + + + + Reactome:R-HSA-9793679 + LUBAC ubiquitinates RIPK1 at K627 + + + + + Reactome:R-HSA-9796346 + MIB2 ubiquitinates RIPK1 at K377, K604, K634 + + + + + Reactome:R-HSA-9796387 + STUB1 ubiquitinates RIPK1 at K571, K604, K627 + + + + + Reactome:R-HSA-9796626 + MIB2 ubiquitinates CFLAR + + + + + Reactome:R-HSA-9815507 + MIB2 ubiquitinates CYLD at K338, K530 + + + + + Reactome:R-HSA-9817362 + SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex + @@ -13427,13 +14012,6 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-983156 Polyubiquitination of substrate - - - - anaphase-promoting complex activity - GOC:dph - GOC:tb - @@ -13469,7 +14047,7 @@ For example, protein A (transcription factor) indirectly increases by expression - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process @@ -13484,7 +14062,7 @@ For example, protein A (transcription factor) indirectly increases by expression - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt @@ -13566,6 +14144,68 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + information content entity + information content entity + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + organism + animal + fungus + plant + virus + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI. + GROUP: OBI Biomaterial Branch + WEB: http://en.wikipedia.org/wiki/Organism + organism + + + + @@ -13719,6 +14359,235 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + + + AAO:0010825 + AEO:0000003 + BILA:0000003 + CARO:0000003 + EHDAA2:0003003 + EMAPA:0 + FBbt:00007001 + FMA:305751 + FMA:67135 + GAID:781 + HAO:0000003 + MA:0003000 + MESH:D000825 + SCTID:362889002 + TAO:0000037 + TGMA:0001823 + VHOG:0001759 + XAO:0003000 + ZFA:0000037 + http://dbpedia.org/ontology/AnatomicalStructure + biological structure + connected biological structure + UBERON:0000061 + + + anatomical structure + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + + + + + connected biological structure + CARO:0000003 + + + + + + + + + A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. + CARO:0001001 + FBbt:00005099 + NLX:147821 + funiculus + nerve fiber bundle + neural fiber bundle + UBERON:0000122 + neuron projection bundle + + + + + A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. + CARO:0001001 + FBC:DOS + FBbt:00005099 + + + + + nerve fiber bundle + FBbt:00005099 + + + + + + + + + + + Anatomical entity that has mass. + + + AAO:0010264 + AEO:0000006 + BILA:0000006 + CARO:0000006 + EHDAA2:0003006 + FBbt:00007016 + FMA:67165 + HAO:0000006 + TAO:0001836 + TGMA:0001826 + VHOG:0001721 + UBERON:0000465 + + + material anatomical entity + + + + + Anatomical entity that has mass. + http://orcid.org/0000-0001-9114-8737 + + + + + + + + + + Anatomical entity that has no mass. + + + AAO:0010265 + AEO:0000007 + BILA:0000007 + CARO:0000007 + EHDAA2:0003007 + FBbt:00007015 + FMA:67112 + HAO:0000007 + TAO:0001835 + TGMA:0001827 + VHOG:0001727 + immaterial physical anatomical entity + UBERON:0000466 + + + immaterial anatomical entity + + + + + Anatomical entity that has no mass. + http://orcid.org/0000-0001-9114-8737 + + + + + immaterial physical anatomical entity + FMA:67112 + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + BIRNLEX:6 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FMA:62955 + HAO:0000000 + MA:0000001 + NCIT:C12219 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + WBbt:0000100 + XAO:0000000 + ZFA:0100000 + UBERON:0001062 + + + anatomical entity + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + FMA:62955 + http://orcid.org/0000-0001-9114-8737 + + + + + UMLS:C1515976 + ncithesaurus:Anatomic_Structure_System_or_Substance + + + + + + + + + An anatomical structure that has more than one cell as a part. + + + CARO:0010000 + FBbt:00100313 + multicellular structure + UBERON:0010000 + + + multicellular anatomical structure + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + + + + + multicellular structure + FBbt:00100313 + + + + @@ -13734,74 +14603,445 @@ For example, protein A (transcription factor) indirectly increases by expression - + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + ready for release + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + pending final vetting + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + requires discussion + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + relation has no temporal argument + + + + + + + + Researcher + Austin Meier + + + + + Researcher + + + + + + Austin Meier + + + + + + + + + researcher + Shawn Zheng Kai Tan + + + + + researcher + + + + + + Shawn Zheng Kai Tan + + + + + + + + + researcher, metadata, diseases, University of Maryland + Lynn Schriml + + + + + researcher, metadata, diseases, University of Maryland + + + + + + Lynn Schriml + + + + + + + + + data scientist + Anne Thessen + + + + + data scientist + + + + + + Anne Thessen + + + + + + + + + researcher + Pier Luigi Buttigieg + + + + + researcher + + + + + + Pier Luigi Buttigieg + + + + + + + + + bioinformatics researcher + Christopher J. Mungall + + + + + bioinformatics researcher + + + + + + Christopher J. Mungall + + + + + + + + + researcher + David Osumi-Sutherland + + + + + researcher + + + + + + David Osumi-Sutherland + + + + + + + + researcher + Lauren E. Chan + + + + + researcher + + + + + + Lauren E. Chan + + - - - - ## Elucidation - -This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + -## How to interpret (informal) + + researcher + Marie-Angélique Laporte + + + + + researcher + + + + + + Marie-Angélique Laporte + + + -First the &quot;atemporal&quot; FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. -## Example + - Class: nucleus - SubClassOf: part_of some cell + + researcher + James P. Balhoff + + + + + researcher + + + + + + James P. Balhoff + + + - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) -## Notes + -This interpretation is *not* the same as an at-all-times relation - axiom holds for all times + + researcher + Lindsay G Cowell + + + + researcher + + + + + + Lindsay G Cowell + + - - - - ## Elucidation + -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. + + researcher + Anna Maria Masci + + + + + researcher + + + + + + Anna Maria Masci + + + -## Example: - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm + - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - relation has no temporal argument + + American chemist + Charles Tapley Hoyt + + + + American chemist + + + + + + Charles Tapley Hoyt + + @@ -13813,25 +15053,404 @@ binary, and takes no temporal argument. /////////////////////////////////////////////////////////////////////////////////////// --> - - - curation status specification + + data item + data item - - - ready for release + + data about an ontology part + Data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part - - - pending final vetting + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolete_core + obsolescence reason specification + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot obsolescence reason specification - + + placeholder removed + placeholder removed + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + ontology term requester - requires discussion + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + denotator type + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + is denotator type + Relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + antisymmetric property + part_of antisymmetric property xsd:true + Use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + has ID digit count + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + has ID range allocated + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + has ID policy for + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + has ID prefix + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + has associated axiom(nl) + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + has associated axiom(fol) + + + is allocated id range + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + Add as annotation triples in the granting ontology + is allocated id range + + + may be identical to + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + scheduled for obsoletion on or after + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + scheduled for obsoletion on or after + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + has axiom label + + + ontology module + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module + + + base ontology module + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + base ontology module + + + + editors ontology module + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + editors ontology module + + + main release ontology module + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + main release ontology module + + + bridge ontology module + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + bridge ontology module + + + + import ontology module + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + import ontology module + + + + subset ontology module + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + subset ontology module + + + + + curation subset ontology module + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + curation subset ontology module + + + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module + + + single layer ontology module + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + single layer subset ontology module + + + exclusion subset ontology module + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + exclusion subset ontology module + + + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module + + + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module + + + + reasoned ontology module + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + reasoned ontology module + + + + generated ontology module + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + generated ontology module + + + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module + + + + + + taxonomic bridge ontology module + taxonomic bridge ontology module + + + ontology module subsetted by expressivity + ontology module subsetted by expressivity + + + obo basic subset ontology module + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + obo basic subset ontology module + + + + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile + + + EL++ ontology module + EL++ ontology module + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + out of scope + + + This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. + OBO Operations call + + logical characteristic of object property + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initalisms + + abbreviation + + + A synonym type for describing ambiguous synonyms + + ambiguous synonym + + + A synonym type for describing dubious synonyms + + dubious synonym + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + layperson synonym + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + plural form + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + UK spelling synonym + + + A synonym type for common misspellings + + misspelling + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + misnomer @@ -13877,6 +15496,19 @@ binary, and takes no temporal argument. + + + + + + + + + + + + + @@ -13942,13 +15574,13 @@ binary, and takes no temporal argument. - + - + - + @@ -13960,13 +15592,13 @@ binary, and takes no temporal argument. - + - + - + @@ -14642,9 +16274,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14653,9 +16285,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14687,9 +16319,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14698,9 +16330,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14732,9 +16364,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14743,9 +16375,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14777,9 +16409,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14788,9 +16420,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14822,9 +16454,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14833,9 +16465,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14867,7 +16499,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14878,7 +16510,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14895,7 +16527,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14905,7 +16537,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14923,7 +16555,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14934,7 +16566,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14951,7 +16583,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14961,7 +16593,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14978,7 +16610,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14989,7 +16621,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15022,9 +16654,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15033,9 +16665,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15066,9 +16698,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15077,9 +16709,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15110,9 +16742,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15121,9 +16753,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15154,9 +16786,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15165,9 +16797,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15199,8 +16831,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15210,8 +16842,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + diff --git a/ro.json b/ro.json index 27e8538e..f43bfa61 100644 --- a/ro.json +++ b/ro.json @@ -3,24 +3,90 @@ "id" : "http://purl.obolibrary.org/obo/ro.json", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/description", + "pred" : "http://purl.org/dc/terms/description", "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." - }, { - "pred" : "http://purl.org/dc/elements/1.1/title", - "val" : "OBO Relations Ontology" }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/publicdomain/zero/1.0/" + }, { + "pred" : "http://purl.org/dc/terms/title", + "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-02-22" + "val" : "2023-06-28" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-22/ro.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/ro.json" }, "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "pending final vetting" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000078", + "lbl" : "curation status specification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation status specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000266" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "requires discussion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + } + }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", "type" : "CLASS", @@ -44,8 +110,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." - } + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" + }, + "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000006", @@ -57,8 +124,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." - } + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" + }, + "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000016", @@ -83,8 +151,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." - } + "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" + }, + "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", @@ -101,8 +170,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." - } + "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" + }, + "comments" : [ "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000034", @@ -183,6 +253,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -354,6 +427,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { @@ -377,80 +453,6 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000000", - "lbl" : "anatomical entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", - "xrefs" : [ "CAROC:Brownsville2014" ] - }, - "comments" : [ "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000003", - "lbl" : "connected anatomical structure", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." - }, - "comments" : [ "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000006", - "lbl" : "material anatomical entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An anatomical entity that has mass." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000007", - "lbl" : "immaterial anatomical entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Anatomical entity that has no mass." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0001001", - "lbl" : "neuron projection bundle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0001010", - "lbl" : "organism or virus or viroid", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melissa Haendel" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0010000", - "lbl" : "multicellular anatomical structure", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An anatomical structure that has more than one cell as a part." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "djs93" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -556,6 +558,26 @@ "val" : "2013-09-23T16:04:08Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01000739", + "lbl" : "habitat", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An environmental system which can sustain and allow the growth of an ecological population.", + "xrefs" : [ "EnvO:EnvO" ] + }, + "comments" : [ "A habitat's specificity to an ecological population differentiates it from other environment classes." ], + "xrefs" : [ { + "val" : "EcoLexicon:habitat" + }, { + "val" : "LTER:238" + }, { + "val" : "SWEETRealm:Habitat" + }, { + "val" : "https://en.wikipedia.org/wiki/Habitat" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", "lbl" : "derives from part of", @@ -571,7 +593,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", + "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", "xrefs" : [ "GOC:pdt" ] }, "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], @@ -586,13 +608,15 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.", + "val" : "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.", "xrefs" : [ "GOC:BioGRID", "GOC:jh2", "PMID:9635407" ] }, "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "anaphase-promoting complex activity", - "xrefs" : [ "GOC:dph", "GOC:tb" ] + "pred" : "hasBroadSynonym", + "val" : "E2" + }, { + "pred" : "hasBroadSynonym", + "val" : "E3" }, { "pred" : "hasNarrowSynonym", "val" : "ubiquitin conjugating enzyme activity" @@ -608,12 +632,6 @@ }, { "pred" : "hasNarrowSynonym", "val" : "ubiquitin-conjugating enzyme activity" - }, { - "pred" : "hasRelatedSynonym", - "val" : "E2" - }, { - "pred" : "hasRelatedSynonym", - "val" : "E3" } ], "xrefs" : [ { "val" : "KEGG_REACTION:R03876" @@ -807,6 +825,8 @@ "val" : "Reactome:R-HSA-5691108" }, { "val" : "Reactome:R-HSA-5693108" + }, { + "val" : "Reactome:R-HSA-68712" }, { "val" : "Reactome:R-HSA-69598" }, { @@ -836,220 +856,1630 @@ }, { "val" : "Reactome:R-HSA-9628444" }, { - "val" : "Reactome:R-HSA-9645394" + "val" : "Reactome:R-HSA-9645394" + }, { + "val" : "Reactome:R-HSA-9645414" + }, { + "val" : "Reactome:R-HSA-9688831" + }, { + "val" : "Reactome:R-HSA-9701000" + }, { + "val" : "Reactome:R-HSA-9750946" + }, { + "val" : "Reactome:R-HSA-975118" + }, { + "val" : "Reactome:R-HSA-975147" + }, { + "val" : "Reactome:R-HSA-9758604" + }, { + "val" : "Reactome:R-HSA-9793444" + }, { + "val" : "Reactome:R-HSA-9793485" + }, { + "val" : "Reactome:R-HSA-9793679" + }, { + "val" : "Reactome:R-HSA-9796346" + }, { + "val" : "Reactome:R-HSA-9796387" + }, { + "val" : "Reactome:R-HSA-9796626" + }, { + "val" : "Reactome:R-HSA-9815507" + }, { + "val" : "Reactome:R-HSA-9817362" + }, { + "val" : "Reactome:R-HSA-983140" + }, { + "val" : "Reactome:R-HSA-983153" + }, { + "val" : "Reactome:R-HSA-983156" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0005634", + "lbl" : "nucleus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.", + "xrefs" : [ "GOC:go_curators" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cell nucleus" + }, { + "pred" : "hasNarrowSynonym", + "val" : "horsetail nucleus", + "xrefs" : [ "GOC:al", "GOC:mah", "GOC:vw", "PMID:15030757" ] + } ], + "xrefs" : [ { + "val" : "NIF_Subcellular:sao1702920020" + }, { + "val" : "Wikipedia:Cell_nucleus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0008150", + "lbl" : "biological_process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", + "xrefs" : [ "GOC:pdt" ] + }, + "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "biological process" + }, { + "pred" : "hasExactSynonym", + "val" : "physiological process" + }, { + "pred" : "hasRelatedSynonym", + "val" : "single organism process" + }, { + "pred" : "hasRelatedSynonym", + "val" : "single-organism process" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Biological_process" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "jl" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-09-19T15:05:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0016301", + "lbl" : "kinase activity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "comments" : [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "phosphokinase activity" + } ], + "xrefs" : [ { + "val" : "Reactome:R-HSA-6788855" + }, { + "val" : "Reactome:R-HSA-6788867" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0019107", + "lbl" : "myristoyltransferase activity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.", + "xrefs" : [ "GOC:ai" ] + }, + "xrefs" : [ { + "val" : "Reactome:R-HSA-141367" + }, { + "val" : "Reactome:R-HSA-162914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example to be eventually removed" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "lbl" : "data item", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data item" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000030", + "lbl" : "information content entity", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "information content entity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "lbl" : "data about an ontology part", + "meta" : { + "definition" : { + "val" : "Data about an ontology part is a data item about a part of an ontology, for example a term" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data about an ontology part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "failed exploratory term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "lbl" : "editor preferred term", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl" : "example of usage", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example of usage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "lbl" : "in branch", + "meta" : { + "definition" : { + "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "in branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "lbl" : "has curation status", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has curation status" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "lbl" : "term editor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term editor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "lbl" : "alternative label", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like." + }, + "comments" : [ "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "OBO Operations committee" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "lbl" : "definition source", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition source" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "metadata complete" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "organizational term" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ready for release" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "metadata incomplete" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "uncurated" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000224", + "lbl" : "obsolete_core", + "meta" : { + "definition" : { + "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl" : "obsolescence reason specification", + "meta" : { + "definition" : { + "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obsolescence reason specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "placeholder removed" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "terms merged" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term imported" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term split" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has obsolescence reason" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "lbl" : "curator note", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An administrative note of use for a curator but of no use for a user" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curator note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." + }, + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "lbl" : "ontology term requester", + "meta" : { + "definition" : { + "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition." + }, + "comments" : [ "The 'term requester' can credit the person, organization or project who request the ontology term." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology term requester" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "lbl" : "denotator type", + "meta" : { + "definition" : { + "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "universal" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "lbl" : "is denotator type", + "meta" : { + "definition" : { + "val" : "Relates an class defined in an ontology, to the type of it's denotator" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "lbl" : "imported from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "For external terms/classes, the ontology from which the term was imported" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "imported from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "meta" : { + "definition" : { + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "defined class" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "meta" : { + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "named class expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "to be replaced with external ontology term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand expression to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "lbl" : "expand assertion to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand assertion to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "lbl" : "first order logic expression", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "first order logic expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "lbl" : "antisymmetric property", + "meta" : { + "definition" : { + "val" : "Use boolean value xsd:true to indicate that the property is an antisymmetric property" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "antisymmetric property" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part_of antisymmetric property xsd:true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl" : "OBO foundry unique label", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which is unique across the OBO Foundry." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "OBO foundry unique label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBO Foundry " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "lbl" : "has ID digit count", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID digit count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "lbl" : "has ID range allocated to", + "meta" : { + "definition" : { + "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID range allocated" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "lbl" : "has ID policy for", + "meta" : { + "definition" : { + "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID policy for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "lbl" : "has ID prefix", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID prefix" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl" : "elucidation", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "elucidation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Barry Smith" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "lbl" : "has associated axiom(nl)", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(nl)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom associated with a term expressed using natural language" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "lbl" : "has associated axiom(fol)", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(fol)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom expressed in first order logic using CLIF syntax" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "lbl" : "is allocated id range", + "meta" : { + "definition" : { + "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is allocated id range" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "has ontology root term", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ontology root term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Nicolas Matentzoglu" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "lbl" : "may be identical to", + "meta" : { + "definition" : { + "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged." + }, + "comments" : [ "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "may be identical to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "lbl" : "scheduled for obsoletion on or after", + "meta" : { + "definition" : { + "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "scheduled for obsoletion on or after" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall, Jie Zheng" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "lbl" : "has axiom label", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has axiom id" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term replaced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "lbl" : "ontology module", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology file" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "lbl" : "base ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "base ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "lbl" : "editors ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editors ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "lbl" : "main release ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "main release ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "lbl" : "bridge ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bridge ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000005", + "lbl" : "import ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology module that is intended to be imported from another ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "import ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add axioms that indicate this is the output of a module extraction process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "import file" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/extract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000006", + "lbl" : "subset ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology slim" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "subset ontology" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/filter" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000007", + "lbl" : "curation subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation subset ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000008", + "lbl" : "analysis subset ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended for usage in analysis or discovery applications." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "analysis ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000009", + "lbl" : "single layer subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "single layer ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribbon subset" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "lbl" : "exclusion subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "exclusion subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "lbl" : "external import ontology module", + "meta" : { + "definition" : { + "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "external import ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "external import" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "lbl" : "species subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "species subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "taxon subset" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "lbl" : "reasoned ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "reasoned ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "lbl" : "generated ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "generated ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "lbl" : "template generated ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "template generated ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "lbl" : "taxonomic bridge ontology module", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "taxonomic bridge ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "lbl" : "ontology module subsetted by expressivity", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module subsetted by expressivity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "lbl" : "obo basic subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obo basic subset ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "lbl" : "ontology module subsetted by OWL profile", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module subsetted by OWL profile" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "lbl" : "EL++ ontology module", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "EL++ ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0100026", + "lbl" : "organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "animal" }, { - "val" : "Reactome:R-HSA-9645414" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "fungus" }, { - "val" : "Reactome:R-HSA-9688831" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "plant" }, { - "val" : "Reactome:R-HSA-9701000" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "virus" }, { - "val" : "Reactome:R-HSA-975118" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { - "val" : "Reactome:R-HSA-975147" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" }, { - "val" : "Reactome:R-HSA-983140" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." }, { - "val" : "Reactome:R-HSA-983153" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP: OBI Biomaterial Branch" }, { - "val" : "Reactome:R-HSA-983156" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "WEB: http://en.wikipedia.org/wiki/Organism" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005634", - "lbl" : "nucleus", + "id" : "http://purl.obolibrary.org/obo/OGMS_0000031", + "lbl" : "disease", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.", - "xrefs" : [ "GOC:go_curators" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cell nucleus" - }, { - "pred" : "hasNarrowSynonym", - "val" : "horsetail nucleus", - "xrefs" : [ "GOC:al", "GOC:mah", "GOC:vw", "PMID:15030757" ] - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao1702920020" - }, { - "val" : "Wikipedia:Cell_nucleus" - } ] + "val" : "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." + } } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0008150", - "lbl" : "biological_process", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", "meta" : { "definition" : { - "val" : "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", - "xrefs" : [ "GOC:pdt" ] + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "biological process" - }, { - "pred" : "hasExactSynonym", - "val" : "physiological process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single organism process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism process" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Biological_process" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-09-19T15:05:24Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016301", - "lbl" : "kinase activity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0001001", + "lbl" : "logical characteristic of object property", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", - "xrefs" : [ "ISBN:0198506732" ] + "val" : "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL." }, - "comments" : [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "phosphokinase activity" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-6788855" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBO Operations call" }, { - "val" : "Reactome:R-HSA-6788867" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0019107", - "lbl" : "myristoyltransferase activity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.", - "xrefs" : [ "GOC:ai" ] + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "xrefs" : [ { - "val" : "Reactome:R-HSA-141367" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : \n PREFIX : Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." [GOC:BioGRID, GOC:jh2, PMID:9635407] -synonym: "anaphase-promoting complex activity" NARROW [GOC:dph, GOC:tb] -synonym: "E2" RELATED [] -synonym: "E3" RELATED [] +def: "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." [GOC:BioGRID, GOC:jh2, PMID:9635407] +synonym: "E2" BROAD [] +synonym: "E3" BROAD [] synonym: "ubiquitin conjugating enzyme activity" NARROW [] synonym: "ubiquitin ligase activity" NARROW [] synonym: "ubiquitin protein ligase activity" NARROW [] @@ -327,6 +295,7 @@ xref: Reactome:R-HSA-5675470 "BIRC2/3 (cIAP1/2) is autoubiquitinated" xref: Reactome:R-HSA-5684250 "SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2" xref: Reactome:R-HSA-5691108 "SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2" xref: Reactome:R-HSA-5693108 "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains" +xref: Reactome:R-HSA-68712 "The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1" xref: Reactome:R-HSA-69598 "Ubiquitination of phosphorylated Cdc25A" xref: Reactome:R-HSA-741386 "RIP2 induces K63-linked ubiquitination of NEMO" xref: Reactome:R-HSA-75824 "Ubiquitination of Cyclin D1" @@ -337,7 +306,7 @@ xref: Reactome:R-HSA-9013069 "Ubiquitination of DLL/JAG ligands upon binding to xref: Reactome:R-HSA-9013974 "Auto-ubiquitination of TRAF3 within activated TLR3 complex" xref: Reactome:R-HSA-9014342 "K63-linked ubiquitination of RIP1 bound to the activated TLR complex" xref: Reactome:R-HSA-918224 "DDX58 is K63 polyubiquitinated" -xref: Reactome:R-HSA-936412 "RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS" +xref: Reactome:R-HSA-936412 "RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS" xref: Reactome:R-HSA-936942 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2" xref: Reactome:R-HSA-936986 "Activated TRAF6 synthesizes unanchored polyubiquitin chains" xref: Reactome:R-HSA-9628444 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation" @@ -345,8 +314,18 @@ xref: Reactome:R-HSA-9645394 "Activated TRAF6 synthesizes unanchored polyubiquit xref: Reactome:R-HSA-9645414 "Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer" xref: Reactome:R-HSA-9688831 "STUB1 ubiquitinates RIPK3 at K55, K363" xref: Reactome:R-HSA-9701000 "BRCA1:BARD1 heterodimer autoubiquitinates" +xref: Reactome:R-HSA-9750946 "TRAF2,6 ubiquitinates NLRC5" xref: Reactome:R-HSA-975118 "TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex" xref: Reactome:R-HSA-975147 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane" +xref: Reactome:R-HSA-9758604 "Ubiquitination of IKBKG by TRAF6" +xref: Reactome:R-HSA-9793444 "ITCH polyubiquitinates MLKL at K50" +xref: Reactome:R-HSA-9793485 "PRKN polyubiquitinates RIPK3" +xref: Reactome:R-HSA-9793679 "LUBAC ubiquitinates RIPK1 at K627" +xref: Reactome:R-HSA-9796346 "MIB2 ubiquitinates RIPK1 at K377, K604, K634" +xref: Reactome:R-HSA-9796387 "STUB1 ubiquitinates RIPK1 at K571, K604, K627" +xref: Reactome:R-HSA-9796626 "MIB2 ubiquitinates CFLAR" +xref: Reactome:R-HSA-9815507 "MIB2 ubiquitinates CYLD at K338, K530" +xref: Reactome:R-HSA-9817362 "SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex" xref: Reactome:R-HSA-983140 "Transfer of Ub from E2 to substrate and release of E2" xref: Reactome:R-HSA-983153 "E1 mediated ubiquitin activation" xref: Reactome:R-HSA-983156 "Polyubiquitination of substrate" @@ -364,7 +343,7 @@ xref: Wikipedia:Cell_nucleus [Term] id: GO:0008150 name: biological_process -def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] @@ -392,6 +371,39 @@ xref: Reactome:R-HSA-141367 "Myristoylation of tBID by NMT1" xref: Reactome:R-HSA-162914 "Myristoylation of Nef" is_a: GO:0003674 ! molecular_function +[Term] +id: IAO:0000030 +name: information content entity +is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000111 "information content entity" xsd:string + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 "GROUP:OBI:" xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: OBI:0100026 +name: organism +def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000111 "organism" xsd:string +property_value: IAO:0000112 "animal" xsd:string +property_value: IAO:0000112 "fungus" xsd:string +property_value: IAO:0000112 "plant" xsd:string +property_value: IAO:0000112 "virus" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" xsd:string +property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string +property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string +property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string + [Term] id: OGMS:0000031 name: disease @@ -472,6 +484,136 @@ property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in htt property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string +[Term] +id: UBERON:0000061 +name: anatomical structure +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003] +subset: common_anatomy +subset: upper_level +synonym: "biological structure" EXACT [] +synonym: "connected biological structure" EXACT [CARO:0000003] +xref: AAO:0010825 +xref: AEO:0000003 +xref: BILA:0000003 +xref: CARO:0000003 +xref: EHDAA2:0003003 +xref: EMAPA:0 +xref: FBbt:00007001 +xref: FMA:305751 +xref: FMA:67135 +xref: GAID:781 +xref: HAO:0000003 +xref: http://dbpedia.org/ontology/AnatomicalStructure +xref: MA:0003000 +xref: MESH:D000825 +xref: SCTID:362889002 +xref: TAO:0000037 +xref: TGMA:0001823 +xref: VHOG:0001759 +xref: XAO:0003000 +xref: ZFA:0000037 +is_a: UBERON:0000465 ! material anatomical entity +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + +[Term] +id: UBERON:0000122 +name: neuron projection bundle +def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] +synonym: "funiculus" EXACT [] +synonym: "nerve fiber bundle" EXACT [FBbt:00005099] +synonym: "neural fiber bundle" EXACT [] +xref: CARO:0001001 +xref: FBbt:00005099 +xref: NLX:147821 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0000465 +name: material anatomical entity +def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy +subset: upper_level +xref: AAO:0010264 +xref: AEO:0000006 +xref: BILA:0000006 +xref: CARO:0000006 +xref: EHDAA2:0003006 +xref: FBbt:00007016 +xref: FMA:67165 +xref: HAO:0000006 +xref: TAO:0001836 +xref: TGMA:0001826 +xref: VHOG:0001721 +is_a: BFO:0000040 ! material entity +is_a: UBERON:0001062 ! anatomical entity +disjoint_from: UBERON:0000466 ! immaterial anatomical entity +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + +[Term] +id: UBERON:0000466 +name: immaterial anatomical entity +def: "Anatomical entity that has no mass." [http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy +subset: upper_level +synonym: "immaterial physical anatomical entity" EXACT [FMA:67112] +xref: AAO:0010265 +xref: AEO:0000007 +xref: BILA:0000007 +xref: CARO:0000007 +xref: EHDAA2:0003007 +xref: FBbt:00007015 +xref: FMA:67112 +xref: HAO:0000007 +xref: TAO:0001835 +xref: TGMA:0001827 +xref: VHOG:0001727 +is_a: BFO:0000141 ! immaterial entity +is_a: UBERON:0001062 ! anatomical entity +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + +[Term] +id: UBERON:0001062 +name: anatomical entity +def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy +subset: upper_level +xref: AAO:0010841 +xref: AEO:0000000 +xref: BILA:0000000 +xref: BIRNLEX:6 +xref: CARO:0000000 +xref: EHDAA2:0002229 +xref: FBbt:10000000 +xref: FMA:62955 +xref: HAO:0000000 +xref: MA:0000001 +xref: NCIT:C12219 +xref: TAO:0100000 +xref: TGMA:0001822 +xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} +xref: WBbt:0000100 +xref: XAO:0000000 +xref: ZFA:0100000 +is_a: BFO:0000004 ! independent continuant +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + +[Term] +id: UBERON:0010000 +name: multicellular anatomical structure +def: "An anatomical structure that has more than one cell as a part." [CARO:0010000] +subset: common_anatomy +subset: upper_level +synonym: "multicellular structure" EXACT [FBbt:00100313] +xref: CARO:0010000 +xref: FBbt:00100313 +is_a: UBERON:0000061 ! anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + [Term] id: UPHENO:0001001 name: phenotype @@ -504,6 +646,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -608,6 +751,7 @@ property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 @@ -928,6 +1072,7 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true @@ -986,8 +1131,8 @@ id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: RO:0001018 ! contained in [Typedef] @@ -995,8 +1140,8 @@ id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0001001 ! neuron projection bundle +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000122 ! neuron projection bundle inverse_of: RO:0002134 ! innervates [Typedef] @@ -1068,7 +1213,7 @@ name: has regulatory component activity def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] is_a: RO:0002017 ! has component activity is_a: RO:0002334 ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -1078,7 +1223,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002335 ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -1088,7 +1233,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -1097,7 +1242,7 @@ name: has necessary component activity comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. is_a: RO:0002017 ! has component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -1105,7 +1250,7 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1115,7 +1260,7 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002180 ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1123,7 +1268,7 @@ id: RO:0002019 name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] is_a: RO:0002233 ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -1131,7 +1276,7 @@ id: RO:0002020 name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] is_a: RO:0002313 ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] @@ -1139,54 +1284,54 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] id: RO:0002026 name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: RO:0002323 ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -1201,10 +1346,12 @@ is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002082 name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: RO:0002081 ! before or simultaneous with @@ -1309,6 +1456,7 @@ subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: RO:0002091 ! starts during is_a: RO:0002093 ! ends during @@ -1326,12 +1474,12 @@ is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002100 name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron -range: CARO:0000003 ! connected anatomical structure +range: UBERON:0000465 ! material anatomical entity is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -1347,7 +1495,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron -range: CARO:0001001 ! neuron projection bundle +range: UBERON:0000122 ! neuron projection bundle is_a: RO:0002131 ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection @@ -1389,8 +1537,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 ! material anatomical entity -range: CARO:0000006 ! material anatomical entity +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: BFO:0000051 ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -1482,7 +1630,7 @@ id: RO:0002111 name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string -domain: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure range: BFO:0000040 ! material entity [Typedef] @@ -1600,7 +1748,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 ! neuron projection bundle +domain: UBERON:0000122 ! neuron projection bundle is_a: RO:0002131 ! overlaps [Typedef] @@ -1611,7 +1759,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 ! neuron projection bundle +domain: UBERON:0000122 ! neuron projection bundle transitive_over: BFO:0000050 ! part of expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] @@ -1707,7 +1855,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -range: CARO:0001010 ! organism or virus or viroid +range: OBI:0100026 ! organism holds_over_chain: BFO:0000050 RO:0002162 holds_over_chain: BFO:0000051 RO:0002162 holds_over_chain: RO:0002202 RO:0002162 @@ -1761,8 +1909,8 @@ id: RO:0002177 name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1880,7 +2028,7 @@ property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant -range: CARO:0000006 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of @@ -2134,7 +2282,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 ! anatomical entity +domain: UBERON:0001062 ! anatomical entity holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by @@ -2212,6 +2360,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: RO:0002224 RO:0002233 is_a: RO:0000057 ! has participant @@ -2228,6 +2377,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: RO:0002230 RO:0002234 is_a: RO:0000057 ! has participant inverse_of: RO:0002353 ! output of @@ -2351,8 +2501,8 @@ def: "x has developmental contribution from y iff x has some part z such that z property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 ! anatomical entity -range: CARO:0000000 ! anatomical entity +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -2381,8 +2531,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 ! material anatomical entity -range: CARO:0000006 ! material anatomical entity +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002257 ! developmentally induces @@ -2444,7 +2594,7 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -2488,7 +2638,7 @@ inverse_of: RO:0002293 ! ubiquitously expresses [Typedef] id: RO:0002292 name: expresses -def: "Inverse of 'expressed in'" [] +def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to @@ -2511,7 +2661,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process -range: CARO:0000000 ! anatomical entity +range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] @@ -2610,7 +2760,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 ! organism or virus or viroid +domain: OBI:0100026 ! organism range: ENVO:01000254 ! environmental system is_a: RO:0002321 ! ecologically related to @@ -2623,6 +2773,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -2634,6 +2785,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -2690,7 +2842,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 ! connected anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2757,6 +2909,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: RO:0002216 ! capable of part of is_a: RO:0002329 ! part of structure that is capable of @@ -2773,6 +2926,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -2810,7 +2964,7 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -2834,6 +2988,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to @@ -3063,7 +3218,7 @@ def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! connected anatomical structure +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3074,7 +3229,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! connected anatomical structure +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3211,8 +3366,8 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 ! anatomical entity -range: CARO:0000000 ! anatomical entity +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] @@ -3319,6 +3474,7 @@ def: "p indirectly positively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 @@ -3341,6 +3497,7 @@ def: "p indirectly negatively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true @@ -3380,11 +3537,11 @@ is_a: RO:0002411 ! causally upstream of id: RO:0002413 name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI holds_over_chain: RO:0002402 RO:0002400 is_a: RO:0002412 ! immediately causally upstream of is_a: RO:0002414 ! transitively provides input for @@ -3489,11 +3646,12 @@ is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -4412,8 +4570,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true @@ -4542,8 +4700,8 @@ name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: RO:0002328 ! functionally related to [Typedef] @@ -4583,7 +4741,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -4613,8 +4771,8 @@ name: participates in a biotic-biotic interaction with subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 ! organism or virus or viroid -range: CARO:0001010 ! organism or virus or viroid +domain: OBI:0100026 ! organism +range: OBI:0100026 ! organism is_a: RO:0002437 ! biotically interacts with [Typedef] @@ -4623,8 +4781,8 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 ! connected anatomical structure -range: CARO:0000003 ! connected anatomical structure +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: BFO:0000050 ! part of [Typedef] @@ -4883,6 +5041,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates @@ -4896,6 +5055,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -5170,7 +5330,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: RO:0004008 name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002234 ! has output is_a: RO:0004007 ! has primary input or output @@ -5180,7 +5340,7 @@ creation_date: 2018-12-13T11:26:32Z [Typedef] id: RO:0004009 name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002233 ! has input is_a: RO:0004007 ! has primary input or output @@ -5282,7 +5442,7 @@ id: RO:0004020 name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -5335,7 +5495,7 @@ id: RO:0004025 name: disease causes dysfunction of property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 ! disease -range: CARO:0000006 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: https://orcid.org/0000-0002-6601-2165 @@ -5387,7 +5547,7 @@ creation_date: 2017-12-26T19:50:53Z id: RO:0004030 name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] -range: CARO:0000003 ! connected anatomical structure +range: UBERON:0000061 ! anatomical structure is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -5406,7 +5566,7 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -5417,6 +5577,7 @@ id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -5428,7 +5589,7 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect @@ -5441,7 +5602,7 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect @@ -5452,6 +5613,7 @@ creation_date: 2018-01-26T23:53:22Z id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -5460,6 +5622,7 @@ creation_date: 2018-03-13T23:55:05Z id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -5524,16 +5687,16 @@ is_a: RO:0002445 ! parasitized by id: RO:0008505 name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] -domain: CARO:0001010 ! organism or virus or viroid -range: CARO:0001010 ! organism or virus or viroid +domain: OBI:0100026 ! organism +range: OBI:0100026 ! organism is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0008506 name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -domain: CARO:0001010 ! organism or virus or viroid -range: CARO:0001010 ! organism or virus or viroid +domain: OBI:0100026 ! organism +range: OBI:0100026 ! organism is_symmetric: true is_a: RO:0002321 ! ecologically related to @@ -5550,6 +5713,19 @@ name: has eggs laid on by def: "inverse of lays eggs on" [] is_a: RO:0002619 ! visited by +[Typedef] +id: RO:0008509 +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 ! organism +range: ENVO:01000739 ! habitat +is_a: RO:0002303 ! has habitat + [Typedef] id: RO:0009001 name: has substance added @@ -5589,7 +5765,7 @@ property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity -range: CARO:0001010 ! organism or virus or viroid +range: OBI:0100026 ! organism [Typedef] id: RO:0009005 @@ -5604,7 +5780,7 @@ is_a: RO:0009001 ! has substance added id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 @@ -5781,7 +5957,7 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: RO:0000057 ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -5790,7 +5966,7 @@ name: has small molecule activator def: "a relation between a process and a continuant, in which the process is activated by the small molecule continuant" [] is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -5799,7 +5975,7 @@ name: has small molecule inhibitor def: "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant" [] is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012006 ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -5810,7 +5986,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam is_a: RO:0000057 ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -5818,25 +5994,27 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] id: RO:0012005 name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] id: RO:0012006 name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -5844,7 +6022,7 @@ id: RO:0012007 name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] is_a: RO:0040036 ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -5854,7 +6032,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam is_a: RO:0002592 ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -5863,8 +6041,9 @@ name: constitutively upstream of def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: RO:0002304 ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -5873,8 +6052,9 @@ name: removes input for def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: RO:0002305 ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -5882,7 +6062,7 @@ id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: RO:0002411 ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -5891,7 +6071,7 @@ name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -5901,7 +6081,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -5911,7 +6091,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct is_a: RO:0002110 ! has postsynaptic terminal in is_a: RO:0013001 ! has synaptic IO in region transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -5921,7 +6101,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct is_a: RO:0002113 ! has presynaptic terminal in is_a: RO:0013001 ! has synaptic IO in region transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -5929,7 +6109,7 @@ id: RO:0013004 name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013001 ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -5938,7 +6118,7 @@ name: receives synaptic input throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013002 ! receives synaptic input in region is_a: RO:0013004 ! has synaptic IO throughout -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -5947,7 +6127,7 @@ name: sends synaptic output throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013003 ! sends synaptic output to region is_a: RO:0013004 ! has synaptic IO throughout -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -5960,7 +6140,7 @@ synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location transitive_over: BFO:0000050 ! part of -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -5969,7 +6149,7 @@ name: receives synaptic input from neuron def: "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." [] is_a: RO:0002103 ! synapsed by inverse_of: RO:0013009 ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -5978,7 +6158,7 @@ name: sends synaptic output to cell def: "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." [] comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. is_a: RO:0002120 ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -5986,7 +6166,7 @@ id: RO:0014001 name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] is_a: RO:0004019 ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: RO:0015001 @@ -6020,7 +6200,7 @@ name: has characterizing marker set def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] synonym: "has marker gene combination" EXACT [] synonym: "has marker signature set" EXACT [] -property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000112 "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." xsd:string property_value: IAO:0000112 "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." xsd:string property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string @@ -6077,8 +6257,8 @@ comment: There are frequently two ways to state the same thing: we can say 'sper id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -6087,8 +6267,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -6096,8 +6276,8 @@ is_a: RO:0002104 ! has plasma membrane part [Typedef] id: RO:0016001 name: has phenotype or disease -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -6105,8 +6285,8 @@ property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -6114,10 +6294,10 @@ is_a: RO:0016001 ! has phenotype or disease id: RO:0016004 name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: RO:0002244 ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: RO:0017001 @@ -6132,6 +6312,25 @@ property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-rel holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z +[Typedef] +id: RO:0017003 +name: positively correlated with +def: "A relation between entities in which one increases or decreases as the other does the same." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: IAO:0000118 "directly correlated with" xsd:string +is_reflexive: true +is_symmetric: true +is_a: RO:0002610 ! correlated with + +[Typedef] +id: RO:0017004 +name: negatively correlated with +def: "A relation between entities in which one increases as the other decreases." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: IAO:0000118 "inversely correlated with" xsd:string +is_symmetric: true +is_a: RO:0002610 ! correlated with + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -6158,7 +6357,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003 id: RO:0018027 name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: RO:0002450 ! directly positively regulates activity of @@ -6167,7 +6366,7 @@ is_a: RO:0002450 ! directly positively regulates activity of id: RO:0018028 name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: RO:0002449 ! directly negatively regulates activity of @@ -6176,11 +6375,132 @@ is_a: RO:0002449 ! directly negatively regulates activity of id: RO:0018029 name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: RO:0002449 ! directly negatively regulates activity of +[Typedef] +id: RO:0018030 +name: chemical relationship +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical." xsd:string + +[Typedef] +id: RO:0018031 +name: is direct conjugate base of +def: "A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B." [] +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)" xsd:string +property_value: RO:0002575 RO:0018033 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_a: RO:0018033 ! is deprotonated form of +inverse_of: RO:0018032 ! is direct conjugate acid of + +[Typedef] +id: RO:0018032 +name: is direct conjugate acid of +def: "A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B." [] +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)" xsd:string +property_value: RO:0002575 RO:0018034 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_a: RO:0018034 ! is protonated form of + +[Typedef] +id: RO:0018033 +name: is deprotonated form of +def: "A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." [] +xref: obo:chebi#is_conjugate_base_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "(E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons." xsd:string +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_transitive: true +is_a: RO:0018030 ! chemical relationship +inverse_of: RO:0018034 ! is protonated form of + +[Typedef] +id: RO:0018034 +name: is protonated form of +def: "A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." [] +xref: obo:chebi#is_conjugate_acid_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "(E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons." xsd:string +property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 +is_transitive: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018035 +name: is matched small molecular pair with +def: "A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification.\n\nWhile this is normally called \"matched molecular pair\" in the cheminformatics literaturel, it is labeled as \"matched small molecular pair\" so as to reduce confusion with peptides and other macromolecules, which are also referenced as \"molecules\" in some contexts.\n\nThis relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A.\n\nThis relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C." [] {http://purl.org/dc/terms/source="https://doi.org/10.1021/jm200452d", http://purl.org/dc/terms/source="https://doi.org/10.1002/ddr.21045", http://purl.org/dc/terms/source="https://en.wikipedia.org/wiki/Matched_molecular_pair_analysis"} +synonym: "is matched molecular pair with" EXACT [] +synonym: "is MMP with" EXACT [] +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-02-28T18:53:32Z" xsd:dateTime +property_value: IAO:0000112 "phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol." xsd:string +is_symmetric: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018036 +name: is tautomer of +def: "Two chemicals are tautomers if they can be readily interconverted.\n\nThis commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms." [] +synonym: "is desmotrope of" EXACT [] +xref: obo:chebi#is_tautomer_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38707", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38709"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_symmetric: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018037 +name: is substitutent group from +def: "Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization." [] +xref: obo:chebi#is_substituent_group_from +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:30795", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:58957"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018038 +name: has functional parent +def: "Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. \n\nFor example, the relationship between a salt and a freebased compound is a \"has functional parent\" relationship." [] +xref: obo:chebi#has_functional_parent +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50851", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50854"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018039 +name: is enantiomer of +def: "Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center.\n\nA chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers)." [] +synonym: "is optical isomer of" EXACT [] +xref: obo:chebi#is_enantiomer_of +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:31472"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_symmetric: true +is_a: RO:0018030 ! chemical relationship + +[Typedef] +id: RO:0018040 +name: has parent hydride +def: "Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B." [] +xref: obo:chebi#has_parent_hydride +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime +property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:39106", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:52083"} +property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 +is_a: RO:0018030 ! chemical relationship + [Typedef] id: RO:0019000 name: regulates characteristic @@ -6213,7 +6533,7 @@ id: RO:0019501 name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] is_a: RO:0003304 ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: RO:0040035 diff --git a/ro.owl b/ro.owl index 6d70676e..26104ba3 100644 --- a/ro.owl +++ b/ro.owl @@ -8,6 +8,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:cito="http://purl.org/spar/cito/" + xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" @@ -20,11 +21,11 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - OBO Relations Ontology + + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - 2023-02-22 + OBO Relations Ontology + 2023-06-28 https://github.com/oborel/obo-relations/ @@ -49,82 +50,211 @@ - + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + editor preferred term + - + + example of usage + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage + example of usage + - + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + has curation status + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition + definition - + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + editor note + - + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + term editor + - + + alternative label + + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label + - + + definition source + + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source + - + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + - + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from + - + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + - + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + first order logic expression An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + PERSON:Alan Ruttenberg + first order logic expression @@ -133,7 +263,15 @@ + OBO foundry unique label + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label @@ -141,20 +279,36 @@ - + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + elucidation + - + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + + term replaced by + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by @@ -182,6 +336,7 @@ ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + defined by construct @@ -849,7 +1004,7 @@ Where we have an annotation assertion true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - + nominally disjoint with @@ -908,7 +1063,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:29Z valid_for_go_annotation_extension @@ -920,7 +1075,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:18Z valid_for_go_gp2term @@ -932,7 +1087,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:04:12Z valid_for_go_ontology @@ -944,7 +1099,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:45Z valid_for_gocam @@ -963,6 +1118,22 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + @@ -987,18 +1158,36 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + @@ -1023,12 +1212,24 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -1065,12 +1266,24 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -1106,7 +1319,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + @@ -1122,7 +1341,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + @@ -1130,7 +1355,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + @@ -1146,7 +1377,13 @@ Where we have an annotation assertion + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + @@ -1171,6 +1408,30 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + + + + @@ -1209,12 +1470,35 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + - + has neurotransmitter @@ -3012,7 +3302,7 @@ N1 SubclassOf ( - + @@ -3061,7 +3351,7 @@ N1 SubclassOf ( - + @@ -3202,7 +3492,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3331,8 +3621,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + @@ -3402,8 +3692,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3539,7 +3829,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3561,16 +3851,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - + @@ -3937,7 +4227,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -4064,6 +4354,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has input + https://wiki.geneontology.org/Has_input @@ -4086,6 +4377,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has output + https://wiki.geneontology.org/Has_output @@ -4269,8 +4561,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + @@ -4307,8 +4599,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -4415,7 +4707,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -4481,7 +4773,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - Inverse of 'expressed in' + y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. expresses @@ -4506,7 +4798,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -4635,7 +4927,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -4663,6 +4955,7 @@ where holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -4678,6 +4971,7 @@ where causally upstream of, negative effect + @@ -4761,7 +5055,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -4874,6 +5168,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to + https://wiki.geneontology.org/Contributes_to @@ -4902,6 +5197,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables + https://wiki.geneontology.org/Enables @@ -4973,7 +5269,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -5003,6 +5299,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled by + https://wiki.geneontology.org/Enabled_by @@ -5334,7 +5631,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -5344,7 +5641,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -5355,7 +5652,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -5365,7 +5662,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -5562,8 +5859,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -5748,6 +6045,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5786,6 +6084,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5860,12 +6159,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for directly provides input for (process to process) provides input for + https://wiki.geneontology.org/Provides_input_for @@ -6049,6 +6348,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different enables activity in is active in + https://wiki.geneontology.org/Is_active_in @@ -6063,8 +6363,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -7546,8 +7846,8 @@ the a supports either the existence of b, or the truth value of b. - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -7558,7 +7858,7 @@ the a supports either the existence of b, or the truth value of b. - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -7750,8 +8050,8 @@ the a supports either the existence of b, or the truth value of b. - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -7810,7 +8110,7 @@ the a supports either the existence of b, or the truth value of b. x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + lumen of @@ -7849,8 +8149,8 @@ the a supports either the existence of b, or the truth value of b. - - + + participates in a biotic-biotic interaction with @@ -7863,8 +8163,8 @@ the a supports either the existence of b, or the truth value of b. - - + + inverse of has skeleton @@ -8286,6 +8586,7 @@ the a supports either the existence of b, or the truth value of b. directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -8303,6 +8604,7 @@ the a supports either the existence of b, or the truth value of b. directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -8748,7 +9050,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -8772,7 +9074,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -8915,7 +9217,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -9003,7 +9305,7 @@ Environmental exposures include those imposed by natural environments, experimen - + @@ -9025,8 +9327,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -9049,8 +9351,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -9105,7 +9407,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -9143,7 +9445,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -9161,6 +9463,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -9180,7 +9483,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -9200,7 +9503,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -9213,6 +9516,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -9225,6 +9529,7 @@ Environmental exposures include those imposed by natural environments, experimen 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -9321,8 +9626,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for @@ -9334,8 +9639,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. ecologically co-occurs with @@ -9363,6 +9668,23 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -9413,7 +9735,7 @@ Environmental exposures include those imposed by natural environments, experimen - + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -9463,7 +9785,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -9709,7 +10031,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z has small molecule regulator @@ -9722,7 +10044,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z has small molecule activator @@ -9735,7 +10057,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z has small molecule inhibitor @@ -9747,7 +10069,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z @@ -9762,7 +10084,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z is small molecule regulator of @@ -9775,9 +10097,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -9788,9 +10111,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -9800,7 +10124,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z results in adhesion of @@ -9811,7 +10135,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z @@ -9826,11 +10150,12 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -9840,11 +10165,12 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z removes input for + https://wiki.geneontology.org/Removes_input_for @@ -9854,7 +10180,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -9867,7 +10193,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -9883,7 +10209,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -9901,7 +10227,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z receives synaptic input in region @@ -9918,7 +10244,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z sends synaptic output to region @@ -9930,7 +10256,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z has synaptic IO throughout @@ -9943,7 +10269,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z receives synaptic input throughout @@ -9956,7 +10282,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z sends synaptic output throughout @@ -9973,7 +10299,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -9989,7 +10315,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z receives synaptic input from neuron @@ -10001,7 +10327,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. sends synaptic output to cell @@ -10014,7 +10340,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + disease has infectious agent @@ -10072,7 +10398,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. - + has marker gene combination has marker signature set has characterizing marker set @@ -10197,8 +10523,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + has high plasma membrane amount @@ -10217,8 +10543,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + has low plasma membrane amount @@ -10234,8 +10560,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z has phenotype or disease https://github.com/oborel/obo-relations/issues/478 @@ -10247,8 +10573,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -10261,8 +10587,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z has exposure medium @@ -10288,6 +10614,34 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relation between entities in which one increases or decreases as the other does the same. + directly correlated with + + positively correlated with + + + + + + + + + + + A relation between entities in which one increases as the other decreases. + inversely correlated with + + negatively correlated with + + + + @@ -10333,7 +10687,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + is agonist of @@ -10346,7 +10700,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + is inverse agonist of @@ -10359,13 +10713,243 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + is antagonist of + + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical. + + chemical relationship + + + + + + + + + + pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) + A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B. + + + is direct conjugate base of + + + + + + + + + + neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) + A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B. + + + is direct conjugate acid of + + + + + + + + + + + + (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. + A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_base_of + is deprotonated form of + + + + + + + + + + + (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. + A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_acid_of + is protonated form of + + + + + + + + + + + phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol. + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + 2023-02-28T18:53:32Z + is MMP with + is matched molecular pair with + is matched small molecular pair with + + + + + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + + + + + + + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + Two chemicals are tautomers if they can be readily interconverted. + +This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms. + + 2023-03-18T23:49:31Z + obo:chebi#is_tautomer_of + is desmotrope of + is tautomer of + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + + + + + + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. + + 2023-03-18T23:49:31Z + obo:chebi#is_substituent_group_from + is substitutent group from + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + + + + + + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. + +For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship. + + 2023-03-18T23:49:31Z + obo:chebi#has_functional_parent + has functional parent + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + + + + + + + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. + +A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers). + + 2023-03-18T23:49:31Z + obo:chebi#is_enantiomer_of + is optical isomer of + is enantiomer of + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + + + + + + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. + + 2023-03-18T23:49:31Z + obo:chebi#has_parent_hydride + has parent hydride + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + + + + + + @@ -10422,7 +11006,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + confers susceptibility to condition @@ -12095,7 +12679,7 @@ For example, protein A (transcription factor) indirectly increases by expression Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - dos + 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate @@ -12194,7 +12778,8 @@ For example, protein A (transcription factor) indirectly increases by expression - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -12219,7 +12804,8 @@ For example, protein A (transcription factor) indirectly increases by expression - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -12278,7 +12864,8 @@ For example, protein A (transcription factor) indirectly increases by expression - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -12304,7 +12891,8 @@ For example, protein A (transcription factor) indirectly increases by expression - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant @@ -12351,140 +12939,41 @@ For example, protein A (transcription factor) indirectly increases by expression - + - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CARO:0000000 - Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. - anatomical entity + + - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CAROC:Brownsville2014 - - + - - - Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. - CARO:0000003 - Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. - connected anatomical structure + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CALOHA:TS-2035 + FBbt:00007002 + FMA:68646 + GO:0005623 + KUPO:0000002 + MESH:D002477 + VHOG:0001533 + WBbt:0004017 + XAO:0003012 + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + cell + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CARO:mah + - - - - - - - - - - - - An anatomical entity that has mass. - CARO:0000006 - material anatomical entity - - - - - - - - - - - - - - - - Anatomical entity that has no mass. - CARO:0000007 - immaterial anatomical entity - - - - - - - - - A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. - CARO:0001001 - neuron projection bundle - - - - - - - - - Material anatomical entity that is a member of an individual species or is a viral or viroid particle. - Melissa Haendel - organism or virus or viroid - - - - - - - - - An anatomical structure that has more than one cell as a part. - djs93 - CARO:0010000 - multicellular anatomical structure - - - - - - - - - - - - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CALOHA:TS-2035 - FBbt:00007002 - FMA:68646 - GO:0005623 - KUPO:0000002 - MESH:D002477 - VHOG:0001533 - WBbt:0004017 - XAO:0003012 - The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). - cell - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CARO:mah - - - - - + @@ -12508,7 +12997,6 @@ For example, protein A (transcription factor) indirectly increases by expression - The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. @@ -12552,10 +13040,31 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + An environmental system which can sustain and allow the growth of an ecological population. + EcoLexicon:habitat + LTER:238 + SWEETRealm:Habitat + https://en.wikipedia.org/wiki/Habitat + A habitat's specificity to an ecological population differentiates it from other environment classes. + habitat + + + + + An environmental system which can sustain and allow the growth of an ecological population. + EnvO:EnvO + + + + - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. @@ -12564,7 +13073,7 @@ For example, protein A (transcription factor) indirectly increases by expression - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GOC:pdt @@ -12580,7 +13089,9 @@ For example, protein A (transcription factor) indirectly increases by expression true - Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + E2 + E3 KEGG_REACTION:R03876 Reactome:R-HSA-1169394 Reactome:R-HSA-1169395 @@ -12677,6 +13188,7 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-5684250 Reactome:R-HSA-5691108 Reactome:R-HSA-5693108 + Reactome:R-HSA-68712 Reactome:R-HSA-69598 Reactome:R-HSA-741386 Reactome:R-HSA-75824 @@ -12695,26 +13207,33 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-9645414 Reactome:R-HSA-9688831 Reactome:R-HSA-9701000 + Reactome:R-HSA-9750946 Reactome:R-HSA-975118 Reactome:R-HSA-975147 + Reactome:R-HSA-9758604 + Reactome:R-HSA-9793444 + Reactome:R-HSA-9793485 + Reactome:R-HSA-9793679 + Reactome:R-HSA-9796346 + Reactome:R-HSA-9796387 + Reactome:R-HSA-9796626 + Reactome:R-HSA-9815507 + Reactome:R-HSA-9817362 Reactome:R-HSA-983140 Reactome:R-HSA-983153 Reactome:R-HSA-983156 - anaphase-promoting complex activity ubiquitin conjugating enzyme activity ubiquitin ligase activity ubiquitin protein ligase activity ubiquitin protein-ligase activity ubiquitin-conjugating enzyme activity - E2 - E3 GO:0004842 ubiquitin-protein transferase activity - Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. GOC:BioGRID GOC:jh2 PMID:9635407 @@ -13289,6 +13808,12 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-5693108 TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains + + + + Reactome:R-HSA-68712 + The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1 + @@ -13353,7 +13878,7 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-936412 - RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS + RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS @@ -13397,6 +13922,12 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-9701000 BRCA1:BARD1 heterodimer autoubiquitinates + + + + Reactome:R-HSA-9750946 + TRAF2,6 ubiquitinates NLRC5 + @@ -13409,6 +13940,60 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-975147 Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane + + + + Reactome:R-HSA-9758604 + Ubiquitination of IKBKG by TRAF6 + + + + + Reactome:R-HSA-9793444 + ITCH polyubiquitinates MLKL at K50 + + + + + Reactome:R-HSA-9793485 + PRKN polyubiquitinates RIPK3 + + + + + Reactome:R-HSA-9793679 + LUBAC ubiquitinates RIPK1 at K627 + + + + + Reactome:R-HSA-9796346 + MIB2 ubiquitinates RIPK1 at K377, K604, K634 + + + + + Reactome:R-HSA-9796387 + STUB1 ubiquitinates RIPK1 at K571, K604, K627 + + + + + Reactome:R-HSA-9796626 + MIB2 ubiquitinates CFLAR + + + + + Reactome:R-HSA-9815507 + MIB2 ubiquitinates CYLD at K338, K530 + + + + + Reactome:R-HSA-9817362 + SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex + @@ -13427,13 +14012,6 @@ For example, protein A (transcription factor) indirectly increases by expression Reactome:R-HSA-983156 Polyubiquitination of substrate - - - - anaphase-promoting complex activity - GOC:dph - GOC:tb - @@ -13469,7 +14047,7 @@ For example, protein A (transcription factor) indirectly increases by expression - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process @@ -13484,7 +14062,7 @@ For example, protein A (transcription factor) indirectly increases by expression - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt @@ -13566,6 +14144,68 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + information content entity + information content entity + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + organism + animal + fungus + plant + virus + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI. + GROUP: OBI Biomaterial Branch + WEB: http://en.wikipedia.org/wiki/Organism + organism + + + + @@ -13719,6 +14359,235 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + + + AAO:0010825 + AEO:0000003 + BILA:0000003 + CARO:0000003 + EHDAA2:0003003 + EMAPA:0 + FBbt:00007001 + FMA:305751 + FMA:67135 + GAID:781 + HAO:0000003 + MA:0003000 + MESH:D000825 + SCTID:362889002 + TAO:0000037 + TGMA:0001823 + VHOG:0001759 + XAO:0003000 + ZFA:0000037 + http://dbpedia.org/ontology/AnatomicalStructure + biological structure + connected biological structure + UBERON:0000061 + + + anatomical structure + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + + + + + connected biological structure + CARO:0000003 + + + + + + + + + A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. + CARO:0001001 + FBbt:00005099 + NLX:147821 + funiculus + nerve fiber bundle + neural fiber bundle + UBERON:0000122 + neuron projection bundle + + + + + A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. + CARO:0001001 + FBC:DOS + FBbt:00005099 + + + + + nerve fiber bundle + FBbt:00005099 + + + + + + + + + + + Anatomical entity that has mass. + + + AAO:0010264 + AEO:0000006 + BILA:0000006 + CARO:0000006 + EHDAA2:0003006 + FBbt:00007016 + FMA:67165 + HAO:0000006 + TAO:0001836 + TGMA:0001826 + VHOG:0001721 + UBERON:0000465 + + + material anatomical entity + + + + + Anatomical entity that has mass. + http://orcid.org/0000-0001-9114-8737 + + + + + + + + + + Anatomical entity that has no mass. + + + AAO:0010265 + AEO:0000007 + BILA:0000007 + CARO:0000007 + EHDAA2:0003007 + FBbt:00007015 + FMA:67112 + HAO:0000007 + TAO:0001835 + TGMA:0001827 + VHOG:0001727 + immaterial physical anatomical entity + UBERON:0000466 + + + immaterial anatomical entity + + + + + Anatomical entity that has no mass. + http://orcid.org/0000-0001-9114-8737 + + + + + immaterial physical anatomical entity + FMA:67112 + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + BIRNLEX:6 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FMA:62955 + HAO:0000000 + MA:0000001 + NCIT:C12219 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + WBbt:0000100 + XAO:0000000 + ZFA:0100000 + UBERON:0001062 + + + anatomical entity + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + FMA:62955 + http://orcid.org/0000-0001-9114-8737 + + + + + UMLS:C1515976 + ncithesaurus:Anatomic_Structure_System_or_Substance + + + + + + + + + An anatomical structure that has more than one cell as a part. + + + CARO:0010000 + FBbt:00100313 + multicellular structure + UBERON:0010000 + + + multicellular anatomical structure + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + + + + + multicellular structure + FBbt:00100313 + + + + @@ -13734,74 +14603,445 @@ For example, protein A (transcription factor) indirectly increases by expression - + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + ready for release + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + pending final vetting + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + requires discussion + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + relation has no temporal argument + + + + + + + + Researcher + Austin Meier + + + + + Researcher + + + + + + Austin Meier + + + + + + + + + researcher + Shawn Zheng Kai Tan + + + + + researcher + + + + + + Shawn Zheng Kai Tan + + + + + + + + + researcher, metadata, diseases, University of Maryland + Lynn Schriml + + + + + researcher, metadata, diseases, University of Maryland + + + + + + Lynn Schriml + + + + + + + + + data scientist + Anne Thessen + + + + + data scientist + + + + + + Anne Thessen + + + + + + + + + researcher + Pier Luigi Buttigieg + + + + + researcher + + + + + + Pier Luigi Buttigieg + + + + + + + + + bioinformatics researcher + Christopher J. Mungall + + + + + bioinformatics researcher + + + + + + Christopher J. Mungall + + + + + + + + + researcher + David Osumi-Sutherland + + + + + researcher + + + + + + David Osumi-Sutherland + + + + + + + + researcher + Lauren E. Chan + + + + + researcher + + + + + + Lauren E. Chan + + - - - - ## Elucidation - -This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + -## How to interpret (informal) + + researcher + Marie-Angélique Laporte + + + + + researcher + + + + + + Marie-Angélique Laporte + + + -First the &quot;atemporal&quot; FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. -## Example + - Class: nucleus - SubClassOf: part_of some cell + + researcher + James P. Balhoff + + + + + researcher + + + + + + James P. Balhoff + + + - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) -## Notes + -This interpretation is *not* the same as an at-all-times relation - axiom holds for all times + + researcher + Lindsay G Cowell + + + + researcher + + + + + + Lindsay G Cowell + + - - - - ## Elucidation + -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. + + researcher + Anna Maria Masci + + + + + researcher + + + + + + Anna Maria Masci + + + -## Example: - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm + - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - relation has no temporal argument + + American chemist + Charles Tapley Hoyt + + + + American chemist + + + + + + Charles Tapley Hoyt + + @@ -13816,25 +15056,404 @@ binary, and takes no temporal argument. /////////////////////////////////////////////////////////////////////////////////////// --> - - - curation status specification + + data item + data item - - - ready for release + + data about an ontology part + Data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part - - - pending final vetting + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolete_core + obsolescence reason specification + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot obsolescence reason specification - + + placeholder removed + placeholder removed + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + ontology term requester - requires discussion + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + denotator type + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + is denotator type + Relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + antisymmetric property + part_of antisymmetric property xsd:true + Use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + has ID digit count + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + has ID range allocated + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + has ID policy for + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + has ID prefix + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + has associated axiom(nl) + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + has associated axiom(fol) + + + is allocated id range + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + Add as annotation triples in the granting ontology + is allocated id range + + + may be identical to + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + scheduled for obsoletion on or after + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + scheduled for obsoletion on or after + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + has axiom label + + + ontology module + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module + + + base ontology module + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + base ontology module + + + + editors ontology module + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + editors ontology module + + + main release ontology module + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + main release ontology module + + + bridge ontology module + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + bridge ontology module + + + + import ontology module + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + import ontology module + + + + subset ontology module + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + subset ontology module + + + + + curation subset ontology module + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + curation subset ontology module + + + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module + + + single layer ontology module + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + single layer subset ontology module + + + exclusion subset ontology module + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + exclusion subset ontology module + + + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module + + + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module + + + + reasoned ontology module + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + reasoned ontology module + + + + generated ontology module + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + generated ontology module + + + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module + + + + + + taxonomic bridge ontology module + taxonomic bridge ontology module + + + ontology module subsetted by expressivity + ontology module subsetted by expressivity + + + obo basic subset ontology module + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + obo basic subset ontology module + + + + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile + + + EL++ ontology module + EL++ ontology module + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + out of scope + + + This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. + OBO Operations call + + logical characteristic of object property + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initalisms + + abbreviation + + + A synonym type for describing ambiguous synonyms + + ambiguous synonym + + + A synonym type for describing dubious synonyms + + dubious synonym + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + layperson synonym + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + plural form + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + UK spelling synonym + + + A synonym type for common misspellings + + misspelling + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + misnomer @@ -13880,6 +15499,19 @@ binary, and takes no temporal argument. + + + + + + + + + + + + + @@ -13945,13 +15577,13 @@ binary, and takes no temporal argument. - + - + - + @@ -13963,13 +15595,13 @@ binary, and takes no temporal argument. - + - + - + @@ -14644,9 +16276,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14655,9 +16287,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14689,9 +16321,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14700,9 +16332,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14734,9 +16366,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14745,9 +16377,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14779,9 +16411,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14790,9 +16422,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14824,9 +16456,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14835,9 +16467,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -14869,7 +16501,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14880,7 +16512,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14897,7 +16529,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14907,7 +16539,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14925,7 +16557,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14936,7 +16568,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14953,7 +16585,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14963,7 +16595,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14980,7 +16612,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14991,7 +16623,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15024,9 +16656,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15035,9 +16667,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15068,9 +16700,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15079,9 +16711,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15112,9 +16744,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15123,9 +16755,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15156,9 +16788,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15167,9 +16799,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -15201,8 +16833,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15212,8 +16844,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl index 45f795ab..b1081d5f 100644 --- a/src/ontology/imports/cl_import.owl +++ b/src/ontology/imports/cl_import.owl @@ -7,10 +7,10 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( "An ontology of cell types.") -Annotation( ) +Annotation( ) Annotation( "Cell Ontology") Annotation( ) Annotation( ) @@ -23,13 +23,13 @@ Annotation( ) Annotation( ) Annotation(rdfs:comment "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo.") -Annotation(owl:versionInfo "2023-02-19") +Annotation(owl:versionInfo "2023-06-22") +Annotation(owl:versionInfo "2023-06-28") -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -67,6 +67,7 @@ AnnotationAssertion( "XAO:0003012") AnnotationAssertion(rdfs:comment "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).") AnnotationAssertion(rdfs:label "cell") +SubClassOf( ) # Class: (sensory neuron) @@ -92,8 +93,6 @@ AnnotationAssertion( "nerve cell") AnnotationAssertion(rdfs:comment "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.") AnnotationAssertion(rdfs:label "neuron") -SubClassOf( ) -SubClassOf( ) SubClassOf( ) diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index 4ff3b62f..ee1e5e75 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -7,15 +7,15 @@ Prefix(rdfs:=) Ontology( - + Annotation( "The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.") -Annotation( ) +Annotation( ) Annotation( "Gene Ontology") Annotation( ) Annotation( "gene_ontology") Annotation( "1.2") -Annotation(owl:versionInfo "2023-01-01") -Annotation(owl:versionInfo "2023-02-19") +Annotation(owl:versionInfo "2023-06-11") +Annotation(owl:versionInfo "2023-06-28") Declaration(Class()) Declaration(Class()) @@ -50,7 +50,7 @@ Declaration(AnnotationProperty( (molecular_function) -AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.") +AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") AnnotationAssertion( "molecular function") AnnotationAssertion( "GO:0003674") AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") @@ -58,7 +58,9 @@ AnnotationAssertion(rdfs:label "mole # Class: (ubiquitin-protein transferase activity) -AnnotationAssertion(Annotation( "GOC:BioGRID") Annotation( "GOC:jh2") Annotation( "PMID:9635407") "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.") +AnnotationAssertion(Annotation( "GOC:BioGRID") Annotation( "GOC:jh2") Annotation( "PMID:9635407") "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.") +AnnotationAssertion( "E2") +AnnotationAssertion( "E3") AnnotationAssertion( "KEGG_REACTION:R03876") AnnotationAssertion(Annotation(rdfs:label "ISGylation of IRF3") "Reactome:R-HSA-1169394") AnnotationAssertion(Annotation(rdfs:label "ISGylation of viral protein NS1") "Reactome:R-HSA-1169395") @@ -155,6 +157,7 @@ AnnotationAssertion(Annotation(rdfs:label "BIRC2/3 (cIAP1/2) is autoubiquitinate AnnotationAssertion(Annotation(rdfs:label "SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2") "Reactome:R-HSA-5684250") AnnotationAssertion(Annotation(rdfs:label "SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2") "Reactome:R-HSA-5691108") AnnotationAssertion(Annotation(rdfs:label "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains") "Reactome:R-HSA-5693108") +AnnotationAssertion(Annotation(rdfs:label "The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1") "Reactome:R-HSA-68712") AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of phosphorylated Cdc25A") "Reactome:R-HSA-69598") AnnotationAssertion(Annotation(rdfs:label "RIP2 induces K63-linked ubiquitination of NEMO") "Reactome:R-HSA-741386") AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of Cyclin D1") "Reactome:R-HSA-75824") @@ -165,7 +168,7 @@ AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of DLL/JAG ligands upo AnnotationAssertion(Annotation(rdfs:label "Auto-ubiquitination of TRAF3 within activated TLR3 complex") "Reactome:R-HSA-9013974") AnnotationAssertion(Annotation(rdfs:label "K63-linked ubiquitination of RIP1 bound to the activated TLR complex") "Reactome:R-HSA-9014342") AnnotationAssertion(Annotation(rdfs:label "DDX58 is K63 polyubiquitinated") "Reactome:R-HSA-918224") -AnnotationAssertion(Annotation(rdfs:label "RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS") "Reactome:R-HSA-936412") +AnnotationAssertion(Annotation(rdfs:label "RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS") "Reactome:R-HSA-936412") AnnotationAssertion(Annotation(rdfs:label "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2") "Reactome:R-HSA-936942") AnnotationAssertion(Annotation(rdfs:label "Activated TRAF6 synthesizes unanchored polyubiquitin chains") "Reactome:R-HSA-936986") AnnotationAssertion(Annotation(rdfs:label "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation") "Reactome:R-HSA-9628444") @@ -173,19 +176,26 @@ AnnotationAssertion(Annotation(rdfs:label "Activated TRAF6 synthesizes unanchore AnnotationAssertion(Annotation(rdfs:label "Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer") "Reactome:R-HSA-9645414") AnnotationAssertion(Annotation(rdfs:label "STUB1 ubiquitinates RIPK3 at K55, K363") "Reactome:R-HSA-9688831") AnnotationAssertion(Annotation(rdfs:label "BRCA1:BARD1 heterodimer autoubiquitinates") "Reactome:R-HSA-9701000") +AnnotationAssertion(Annotation(rdfs:label "TRAF2,6 ubiquitinates NLRC5") "Reactome:R-HSA-9750946") AnnotationAssertion(Annotation(rdfs:label "TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex") "Reactome:R-HSA-975118") AnnotationAssertion(Annotation(rdfs:label "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane") "Reactome:R-HSA-975147") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of IKBKG by TRAF6") "Reactome:R-HSA-9758604") +AnnotationAssertion(Annotation(rdfs:label "ITCH polyubiquitinates MLKL at K50") "Reactome:R-HSA-9793444") +AnnotationAssertion(Annotation(rdfs:label "PRKN polyubiquitinates RIPK3") "Reactome:R-HSA-9793485") +AnnotationAssertion(Annotation(rdfs:label "LUBAC ubiquitinates RIPK1 at K627") "Reactome:R-HSA-9793679") +AnnotationAssertion(Annotation(rdfs:label "MIB2 ubiquitinates RIPK1 at K377, K604, K634") "Reactome:R-HSA-9796346") +AnnotationAssertion(Annotation(rdfs:label "STUB1 ubiquitinates RIPK1 at K571, K604, K627") "Reactome:R-HSA-9796387") +AnnotationAssertion(Annotation(rdfs:label "MIB2 ubiquitinates CFLAR") "Reactome:R-HSA-9796626") +AnnotationAssertion(Annotation(rdfs:label "MIB2 ubiquitinates CYLD at K338, K530") "Reactome:R-HSA-9815507") +AnnotationAssertion(Annotation(rdfs:label "SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex") "Reactome:R-HSA-9817362") AnnotationAssertion(Annotation(rdfs:label "Transfer of Ub from E2 to substrate and release of E2") "Reactome:R-HSA-983140") AnnotationAssertion(Annotation(rdfs:label "E1 mediated ubiquitin activation") "Reactome:R-HSA-983153") AnnotationAssertion(Annotation(rdfs:label "Polyubiquitination of substrate") "Reactome:R-HSA-983156") -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "anaphase-promoting complex activity") AnnotationAssertion( "ubiquitin conjugating enzyme activity") AnnotationAssertion( "ubiquitin ligase activity") AnnotationAssertion( "ubiquitin protein ligase activity") AnnotationAssertion( "ubiquitin protein-ligase activity") AnnotationAssertion( "ubiquitin-conjugating enzyme activity") -AnnotationAssertion( "E2") -AnnotationAssertion( "E3") AnnotationAssertion( "GO:0004842") AnnotationAssertion(rdfs:label "ubiquitin-protein transferase activity") SubClassOf( ) @@ -202,7 +212,7 @@ AnnotationAssertion(rdfs:label "nucl # Class: (biological_process) -AnnotationAssertion(Annotation( "GOC:pdt") "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:05:24Z") AnnotationAssertion( "Wikipedia:Biological_process") diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index 534edad7..5e598187 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-05-27") +Annotation(owl:versionInfo "2023-06-28") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl index 0d8bfd0f..0e0caea9 100644 --- a/src/ontology/imports/omo_import.owl +++ b/src/ontology/imports/omo_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-03-29") + +Annotation(owl:versionInfo "2023-06-28") Declaration(Class()) Declaration(Class()) @@ -41,10 +41,8 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -645,4 +643,32 @@ AnnotationAssertion( "OBO Operations call") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "logical characteristic of object property") +AnnotationAssertion( "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)") +AnnotationAssertion( "A synonym type for describing abbreviations or initalisms") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "abbreviation") +AnnotationAssertion( "A synonym type for describing ambiguous synonyms") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ambiguous synonym") +AnnotationAssertion( "A synonym type for describing dubious synonyms") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "dubious synonym") +AnnotationAssertion( "EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)") +AnnotationAssertion( "A synonym type for describing layperson or colloquial synonyms") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "layperson synonym") +AnnotationAssertion( "CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)") +AnnotationAssertion( "A synonym type for describing pluralization synonyms") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "plural form") +AnnotationAssertion( "CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)") +AnnotationAssertion( "A synonym type for describing UK spelling variants") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "UK spelling synonym") +AnnotationAssertion( "A synonym type for common misspellings") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "misspelling") +AnnotationAssertion( "A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "misnomer") ) \ No newline at end of file diff --git a/src/ontology/imports/orcidio_import.owl b/src/ontology/imports/orcidio_import.owl index c1e8ed4f..9f9c776a 100644 --- a/src/ontology/imports/orcidio_import.owl +++ b/src/ontology/imports/orcidio_import.owl @@ -7,16 +7,21 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-02-28") + +Annotation(owl:versionInfo "2023-06-28") +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -29,6 +34,11 @@ Declaration(AnnotationProperty()) # Named Individuals ############################ +# Individual: (Austin Meier) + +AnnotationAssertion(Annotation( ) "Researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Austin Meier") + # Individual: (Shawn Zheng Kai Tan) AnnotationAssertion(Annotation( ) "researcher") @@ -39,6 +49,11 @@ AnnotationAssertion(Annotation( ) "researcher, metadata, diseases, University of Maryland") AnnotationAssertion(Annotation( ) rdfs:label "Lynn Schriml") +# Individual: (Anne Thessen) + +AnnotationAssertion(Annotation( ) "data scientist") +AnnotationAssertion(Annotation( ) rdfs:label "Anne Thessen") + # Individual: (Pier Luigi Buttigieg) AnnotationAssertion(Annotation( ) "researcher") @@ -54,6 +69,11 @@ AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "David Osumi-Sutherland") +# Individual: (Lauren E. Chan) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Lauren E. Chan") + # Individual: (Marie-Angélique Laporte) AnnotationAssertion(Annotation( ) "researcher") @@ -64,6 +84,16 @@ AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "James P. Balhoff") +# Individual: (Lindsay G Cowell) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Lindsay G Cowell") + +# Individual: (Anna Maria Masci) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Anna Maria Masci") + # Individual: (Charles Tapley Hoyt) AnnotationAssertion(Annotation( ) "American chemist") diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 5380ec89..3ad1e5dd 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -7,16 +7,16 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( "An ontology of phenotypic qualities (properties, attributes or characteristics).") -Annotation( ) +Annotation( ) Annotation( "PATO - the Phenotype And Trait Ontology") Annotation( ) Annotation( "quality") Annotation( "1.2") -Annotation(owl:versionInfo "2023-02-17") -Annotation(owl:versionInfo "2023-02-19") +Annotation(owl:versionInfo "2023-05-18") +Annotation(owl:versionInfo "2023-06-28") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index 05a49e66..57a32020 100644 --- a/src/ontology/imports/uberon_import.owl +++ b/src/ontology/imports/uberon_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( ) Annotation( ) @@ -36,7 +36,7 @@ Annotation( ) Annotation( ) Annotation( ) -Annotation( ) +Annotation( ) Annotation( ) Annotation( ) Annotation( ) @@ -68,7 +68,7 @@ Annotation( "PMID:16417468 Forgotten and Annotation( "aggregates AAO from 13:04:2012") Annotation( "aggregates TAO from 09:08:2012") Annotation( "aggregates VSAO from 16:07:2012") -Annotation(owl:versionInfo "2023-06-01") +Annotation(owl:versionInfo "2023-06-28") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 460f331a..dc670af3 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -1261,7 +1261,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000050 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000050 obo:valid_for_gocam) AnnotationAssertion(rdfs:seeAlso obo:BFO_0000050 ) AnnotationAssertion(rdfs:seeAlso obo:BFO_0000050 ) -AnnotationAssertion(rdfs:seeAlso obo:BFO_0000050 ) +AnnotationAssertion(rdfs:seeAlso obo:BFO_0000050 "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) SubObjectPropertyOf(obo:BFO_0000050 obo:RO_0002131) # Object Property: obo:BFO_0000051 (has part) @@ -1285,7 +1285,7 @@ SubObjectPropertyOf(obo:BFO_0000063 obo:RO_0002222) AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000066 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000066 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000066 obo:valid_for_gocam) -AnnotationAssertion(rdfs:seeAlso obo:BFO_0000066 ) +AnnotationAssertion(rdfs:seeAlso obo:BFO_0000066 "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) # Object Property: obo:RO_0000052 (characteristic of) @@ -1386,7 +1386,7 @@ ObjectPropertyRange(obo:RO_0001023 obo:BFO_0000040) # Object Property: obo:RO_0001025 (located in) AnnotationAssertion(oboInOwl:inSubset obo:RO_0001025 obo:valid_for_go_gp2term) -AnnotationAssertion(rdfs:seeAlso obo:RO_0001025 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0001025 "https://wiki.geneontology.org/Located_in"^^xsd:anyURI) # Object Property: obo:RO_0002000 (2D boundary of) @@ -1682,7 +1682,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002092 obo:valid_for_go_annotation AnnotationAssertion(oboInOwl:inSubset obo:RO_0002092 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002092 obo:valid_for_gocam) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002092 subsets:ro-eco) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002092 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002092 "https://wiki.geneontology.org/Happens_during"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002092 obo:RO_0002091) # Object Property: obo:RO_0002100 (has soma location) @@ -2590,7 +2590,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002233 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002233 obo:valid_for_gocam) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002233 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002233 "has input"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002233 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002233 "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002233 obo:RO_0000057) InverseObjectProperties(obo:RO_0002233 obo:RO_0002352) ObjectPropertyDomain(obo:RO_0002233 obo:BFO_0000015) @@ -2606,7 +2606,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002234 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002234 obo:valid_for_gocam) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002234 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002234 "has output"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002234 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002234 "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002234 obo:RO_0000057) InverseObjectProperties(obo:RO_0002234 obo:RO_0002353) @@ -2821,8 +2821,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002264 "c acts upstream of or within AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:RO_0002264 "affects") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002264 obo:valid_for_go_gp2term) AnnotationAssertion(rdfs:label obo:RO_0002264 "acts upstream of or within") -AnnotationAssertion(rdfs:seeAlso obo:RO_0002264 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002264 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002264 "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002264 obo:RO_0002500) # Object Property: obo:RO_0002285 (developmentally replaces) @@ -3145,7 +3144,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002326 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002326 "https://wiki.geneontology.org/Contributes_to"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002326 obo:RO_0002216) SubObjectPropertyOf(obo:RO_0002326 obo:RO_0002329) @@ -3162,7 +3161,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:RO_0002327 "is executing") AnnotationAssertion(obo:IAO_0000232 obo:RO_0002327 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002327 obo:valid_for_go_gp2term) AnnotationAssertion(rdfs:label obo:RO_0002327 "enables"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002327 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002327 "https://wiki.geneontology.org/Enables"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002327 obo:RO_0002215) InverseObjectProperties(obo:RO_0002327 obo:RO_0002333) @@ -3197,8 +3196,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002331 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002331 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002331 "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002331 obo:RO_0000056) SubObjectPropertyOf(obo:RO_0002331 obo:RO_0002431) @@ -3220,7 +3218,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002333 "inverse of enables") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002333 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002333 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0002333 "enabled by"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002333 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002333 "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002333 obo:RO_0000057) SubObjectPropertyOf(obo:RO_0002333 obo:RO_0002328) @@ -3685,7 +3683,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002407 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002407 "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002407 obo:RO_0002213) SubObjectPropertyOf(obo:RO_0002407 obo:RO_0012012) TransitiveObjectProperty(obo:RO_0002407) @@ -3704,7 +3702,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002409 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002409 "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002409 obo:RO_0002212) SubObjectPropertyOf(obo:RO_0002409 obo:RO_0012012) TransitiveObjectProperty(obo:RO_0002409) @@ -3759,7 +3757,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:RO_0002413 "directly provides input for" AnnotationAssertion(obo:IAO_0000119 obo:RO_0002413 ) AnnotationAssertion(obo:IAO_0000589 obo:RO_0002413 "directly provides input for (process to process)") AnnotationAssertion(rdfs:label obo:RO_0002413 "provides input for"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002413 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002413 "https://wiki.geneontology.org/Provides_input_for"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002413 obo:RO_0002412) SubObjectPropertyOf(obo:RO_0002413 obo:RO_0002414) @@ -3864,7 +3862,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:RO_0002432 "executes activity in") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002432 "enables activity in") AnnotationAssertion(rdfs:comment obo:RO_0002432 "") AnnotationAssertion(rdfs:label obo:RO_0002432 "is active in") -AnnotationAssertion(rdfs:seeAlso obo:RO_0002432 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002432 "https://wiki.geneontology.org/Is_active_in"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002432 obo:RO_0002131) SubObjectPropertyOf(obo:RO_0002432 obo:RO_0002328) @@ -5242,7 +5240,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002629 obo:valid_for_go_annotation AnnotationAssertion(oboInOwl:inSubset obo:RO_0002629 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002629 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0002629 "directly positively regulates") -AnnotationAssertion(rdfs:seeAlso obo:RO_0002629 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002629 "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002629 obo:RO_0002213) SubObjectPropertyOf(obo:RO_0002629 obo:RO_0002578) @@ -5256,7 +5254,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002630 obo:valid_for_go_annotation AnnotationAssertion(oboInOwl:inSubset obo:RO_0002630 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002630 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0002630 "directly negatively regulates") -AnnotationAssertion(rdfs:seeAlso obo:RO_0002630 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0002630 "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002630 obo:RO_0002212) SubObjectPropertyOf(obo:RO_0002630 obo:RO_0002578) @@ -5776,8 +5774,7 @@ AnnotationAssertion(oboInOwl:created_by obo:RO_0004032 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0004032 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0004032 "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0004032 obo:RO_0002264) # Object Property: obo:RO_0004033 (acts upstream of or within, negative effect) @@ -5787,7 +5784,7 @@ AnnotationAssertion(oboInOwl:created_by obo:RO_0004033 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0004033 "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0004033 obo:RO_0002264) # Object Property: obo:RO_0004034 (acts upstream of, positive effect) @@ -5798,8 +5795,7 @@ AnnotationAssertion(oboInOwl:created_by obo:RO_0004034 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0004034 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0004034 "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0004034 obo:RO_0002263) SubObjectPropertyOf(obo:RO_0004034 obo:RO_0004032) @@ -5811,8 +5807,7 @@ AnnotationAssertion(oboInOwl:created_by obo:RO_0004035 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0004035 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0004035 "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0004035 obo:RO_0002263) SubObjectPropertyOf(obo:RO_0004035 obo:RO_0004033) @@ -5822,7 +5817,7 @@ AnnotationAssertion(obo:RO_0004050 obo:RO_0004046 obo:RO_0002418) AnnotationAssertion(oboInOwl:created_by obo:RO_0004046 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0004046 "2018-03-13T23:55:05Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0004046 "causally upstream of or within, negative effect") -AnnotationAssertion(rdfs:seeAlso obo:RO_0004046 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0004046 "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0004046 obo:RO_0002418) # Object Property: obo:RO_0004047 (causally upstream of or within, positive effect) @@ -6204,7 +6199,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0012005 "a relation between a continu AnnotationAssertion(oboInOwl:created_by obo:RO_0012005 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012005 "2020-06-24T13:15:26Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012005 "is small molecule activator of"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0012005 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0012005 "https://wiki.geneontology.org/Is_small_molecule_activator_of"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0012005 obo:RO_0002598) SubObjectPropertyOf(obo:RO_0012005 obo:RO_0012004) @@ -6214,7 +6209,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0012006 "a relation between a continu AnnotationAssertion(oboInOwl:created_by obo:RO_0012006 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012006 "2020-06-24T13:15:35Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012006 "is small molecule inhibitor of"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0012006 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0012006 "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0012006 obo:RO_0002597) SubObjectPropertyOf(obo:RO_0012006 obo:RO_0012004) @@ -6244,7 +6239,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:RO_0012009 "2022-09-26T06:01:01Z" AnnotationAssertion(oboInOwl:inSubset obo:RO_0012009 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012009 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0012009 "constitutively upstream of"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0012009 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0012009 "https://wiki.geneontology.org/Constitutively_upstream_of"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0012009 obo:RO_0002304) # Object Property: obo:RO_0012010 (removes input for) @@ -6255,7 +6250,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:RO_0012010 "2022-09-26T06:06:20Z" AnnotationAssertion(oboInOwl:inSubset obo:RO_0012010 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012010 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0012010 "removes input for"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0012010 ) +AnnotationAssertion(rdfs:seeAlso obo:RO_0012010 "https://wiki.geneontology.org/Removes_input_for"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0012010 obo:RO_0002305) # Object Property: obo:RO_0012011 (indirectly causally upstream of) @@ -6614,7 +6609,7 @@ This is a transitive relationship and follows this design pattern: https://obore AnnotationAssertion(dc:creator obo:RO_0018033 ) AnnotationAssertion(rdfs:label obo:RO_0018033 "is deprotonated form of") AnnotationAssertion(rdfs:seeAlso obo:RO_0018033 ) -AnnotationAssertion(skos:exactMatch obo:RO_0018033 ) +AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018033 "obo:chebi#is_conjugate_base_of") SubObjectPropertyOf(obo:RO_0018033 obo:RO_0018030) InverseObjectProperties(obo:RO_0018033 obo:RO_0018034) TransitiveObjectProperty(obo:RO_0018033) @@ -6628,7 +6623,7 @@ This is a transitive relationship and follows this design pattern: https://obore AnnotationAssertion(dc:creator obo:RO_0018034 ) AnnotationAssertion(rdfs:label obo:RO_0018034 "is protonated form of") AnnotationAssertion(rdfs:seeAlso obo:RO_0018034 ) -AnnotationAssertion(skos:exactMatch obo:RO_0018034 ) +AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018034 "obo:chebi#is_conjugate_acid_of") SubObjectPropertyOf(obo:RO_0018034 obo:RO_0018030) TransitiveObjectProperty(obo:RO_0018034) @@ -6661,7 +6656,7 @@ AnnotationAssertion(dc:date obo:RO_0018036 "2023-03-18T23:49:31Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0018036 "is desmotrope of") AnnotationAssertion(rdfs:label obo:RO_0018036 "is tautomer of"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0018036 ) -AnnotationAssertion(skos:exactMatch obo:RO_0018036 ) +AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018036 "obo:chebi#is_tautomer_of") SubObjectPropertyOf(obo:RO_0018036 obo:RO_0018030) SymmetricObjectProperty(obo:RO_0018036) @@ -6673,7 +6668,7 @@ AnnotationAssertion(dc:creator obo:RO_0018037 ) -AnnotationAssertion(skos:exactMatch obo:RO_0018037 ) +AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018037 "obo:chebi#is_substituent_group_from") SubObjectPropertyOf(obo:RO_0018037 obo:RO_0018030) # Object Property: obo:RO_0018038 (has functional parent) @@ -6686,7 +6681,7 @@ AnnotationAssertion(dc:creator obo:RO_0018038 ) -AnnotationAssertion(skos:exactMatch obo:RO_0018038 ) +AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018038 "obo:chebi#has_functional_parent") SubObjectPropertyOf(obo:RO_0018038 obo:RO_0018030) # Object Property: obo:RO_0018039 (is enantiomer of) @@ -6700,7 +6695,7 @@ AnnotationAssertion(dc:date obo:RO_0018039 "2023-03-18T23:49:31Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0018039 "is optical isomer of") AnnotationAssertion(rdfs:label obo:RO_0018039 "is enantiomer of"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0018039 ) -AnnotationAssertion(skos:exactMatch obo:RO_0018039 ) +AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018039 "obo:chebi#is_enantiomer_of") SubObjectPropertyOf(obo:RO_0018039 obo:RO_0018030) SymmetricObjectProperty(obo:RO_0018039) @@ -6712,7 +6707,7 @@ AnnotationAssertion(dc:creator obo:RO_0018040 ) -AnnotationAssertion(skos:exactMatch obo:RO_0018040 ) +AnnotationAssertion(oboInOwl:hasDbXref obo:RO_0018040 "obo:chebi#has_parent_hydride") SubObjectPropertyOf(obo:RO_0018040 obo:RO_0018030) # Object Property: obo:RO_0019000 (regulates characteristic) diff --git a/src/ontology/subsets/ro-causal.json b/src/ontology/subsets/ro-causal.json index 7e8d7fb2..8b89b440 100644 --- a/src/ontology/subsets/ro-causal.json +++ b/src/ontology/subsets/ro-causal.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index 87ecf23c..942e3a70 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index bada75b7..716fd015 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-causal.tsv b/src/ontology/subsets/ro-causal.tsv index 49389a06..b039df98 100644 --- a/src/ontology/subsets/ro-causal.tsv +++ b/src/ontology/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid1 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid18 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid22 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid26 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid33 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid37 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid40 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid5 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid52 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid58 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid61 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid64 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid67 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid9 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid1 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid18 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid22 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid26 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid33 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid37 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid40 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid5 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid52 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid58 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid61 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid64 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid67 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid9 @@ -26,19 +26,14 @@ _:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid9 + + + + + + diff --git a/src/ontology/subsets/ro-chado.json b/src/ontology/subsets/ro-chado.json index 93184cd1..f86a1d5d 100644 --- a/src/ontology/subsets/ro-chado.json +++ b/src/ontology/subsets/ro-chado.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-02-22" + "val" : "2023-06-28" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-22/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -74,6 +74,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -181,173 +184,1443 @@ "deprecated" : true } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occurs_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", + "lbl" : "derives from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example to be eventually removed" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "lbl" : "data item", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data item" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "lbl" : "data about an ontology part", + "meta" : { + "definition" : { + "val" : "Data about an ontology part is a data item about a part of an ontology, for example a term" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data about an ontology part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "failed exploratory term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "lbl" : "editor preferred term", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl" : "example of usage", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example of usage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "lbl" : "in branch", + "meta" : { + "definition" : { + "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "in branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "lbl" : "has curation status", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has curation status" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "lbl" : "term editor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term editor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "lbl" : "alternative label", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like." + }, + "comments" : [ "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "OBO Operations committee" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "lbl" : "definition source", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition source" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "metadata complete" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "organizational term" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ready for release" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "metadata incomplete" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "uncurated" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "pending final vetting" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000224", + "lbl" : "obsolete_core", + "meta" : { + "definition" : { + "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl" : "obsolescence reason specification", + "meta" : { + "definition" : { + "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obsolescence reason specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "placeholder removed" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "terms merged" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term imported" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term split" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has obsolescence reason" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "lbl" : "curator note", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An administrative note of use for a curator but of no use for a user" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curator note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." + }, + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "lbl" : "ontology term requester", + "meta" : { + "definition" : { + "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition." + }, + "comments" : [ "The 'term requester' can credit the person, organization or project who request the ontology term." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology term requester" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "lbl" : "denotator type", + "meta" : { + "definition" : { + "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "universal" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "lbl" : "is denotator type", + "meta" : { + "definition" : { + "val" : "Relates an class defined in an ontology, to the type of it's denotator" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "lbl" : "imported from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "For external terms/classes, the ontology from which the term was imported" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "imported from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "meta" : { + "definition" : { + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "defined class" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "meta" : { + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "named class expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "to be replaced with external ontology term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand expression to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "lbl" : "expand assertion to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand assertion to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "lbl" : "first order logic expression", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "first order logic expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "lbl" : "antisymmetric property", + "meta" : { + "definition" : { + "val" : "Use boolean value xsd:true to indicate that the property is an antisymmetric property" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "antisymmetric property" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part_of antisymmetric property xsd:true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "requires discussion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl" : "OBO foundry unique label", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which is unique across the OBO Foundry." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "OBO foundry unique label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBO Foundry " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "lbl" : "has ID digit count", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID digit count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "lbl" : "has ID range allocated to", + "meta" : { + "definition" : { + "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID range allocated" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "lbl" : "has ID policy for", + "meta" : { + "definition" : { + "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID policy for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "lbl" : "has ID prefix", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID prefix" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl" : "elucidation", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "elucidation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Barry Smith" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "lbl" : "has associated axiom(nl)", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(nl)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom associated with a term expressed using natural language" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "lbl" : "has associated axiom(fol)", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(fol)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom expressed in first order logic using CLIF syntax" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "lbl" : "is allocated id range", + "meta" : { + "definition" : { + "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is allocated id range" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "has ontology root term", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ontology root term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Nicolas Matentzoglu" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "lbl" : "may be identical to", + "meta" : { + "definition" : { + "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged." + }, + "comments" : [ "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "may be identical to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "lbl" : "scheduled for obsoletion on or after", + "meta" : { + "definition" : { + "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "scheduled for obsoletion on or after" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall, Jie Zheng" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "lbl" : "has axiom label", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has axiom id" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term replaced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "lbl" : "ontology module", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology file" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "lbl" : "base ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "base ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "lbl" : "editors ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editors ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "lbl" : "main release ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "main release ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "lbl" : "bridge ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bridge ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000005", + "lbl" : "import ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology module that is intended to be imported from another ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "import ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add axioms that indicate this is the output of a module extraction process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "import file" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/extract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000006", + "lbl" : "subset ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology slim" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "subset ontology" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/filter" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000007", + "lbl" : "curation subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation subset ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000008", + "lbl" : "analysis subset ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended for usage in analysis or discovery applications." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "analysis ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000009", + "lbl" : "single layer subset ontology module", "meta" : { "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" + "val" : "single layer ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + "val" : "ribbon subset" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "lbl" : "exclusion subset ontology module", "meta" : { "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" + "val" : "exclusion subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "lbl" : "external import ontology module", "meta" : { "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" + "val" : "external import ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" + "val" : "external import" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "lbl" : "species subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "species subset ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" + "val" : "taxon subset" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "lbl" : "reasoned ontology module", "meta" : { "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" + "val" : "reasoned ontology module" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", - "lbl" : "derives from part of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "lbl" : "generated ontology module", "meta" : { "definition" : { - "val" : "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." - } + "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "generated ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000078", - "lbl" : "curation status specification", + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "lbl" : "template generated ontology module", "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "template generated ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "lbl" : "taxonomic bridge ontology module", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "taxonomic bridge ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "lbl" : "ontology module subsetted by expressivity", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module subsetted by expressivity" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000225", - "lbl" : "obsolescence reason specification", + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "lbl" : "obo basic subset ontology module", "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obo basic subset ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000426", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "lbl" : "ontology module subsetted by OWL profile", "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." - } + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module subsetted by OWL profile" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "lbl" : "EL++ ontology module", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "EL++ ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000589", - "lbl" : "OBO foundry unique label", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", "meta" : { + "definition" : { + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/OMO_0001001", + "lbl" : "logical characteristic of object property", "meta" : { + "definition" : { + "val" : "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBO Operations call" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -361,6 +1634,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : - - 2023-02-22 + + 2023-06-28 @@ -45,82 +46,211 @@ - + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + editor preferred term + - + + example of usage + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage + example of usage + - + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + has curation status + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition + definition - + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + editor note + - + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + term editor + - + + alternative label + + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label + - + + definition source + + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source + - + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + - + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from + - + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + - + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + first order logic expression An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + PERSON:Alan Ruttenberg + first order logic expression @@ -129,7 +259,15 @@ + OBO foundry unique label + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label @@ -137,20 +275,36 @@ - + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + elucidation + - + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + + term replaced by + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by @@ -178,6 +332,7 @@ ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + defined by construct @@ -845,7 +1000,7 @@ Where we have an annotation assertion true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - + nominally disjoint with @@ -904,7 +1059,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:29Z valid_for_go_annotation_extension @@ -916,7 +1071,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:18Z valid_for_go_gp2term @@ -928,7 +1083,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:04:12Z valid_for_go_ontology @@ -940,7 +1095,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:45Z valid_for_gocam @@ -959,6 +1114,22 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + @@ -983,18 +1154,36 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + @@ -1019,12 +1208,24 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -1061,12 +1262,24 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -1102,7 +1315,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + @@ -1118,7 +1337,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + @@ -1126,7 +1351,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + @@ -1142,7 +1373,13 @@ Where we have an annotation assertion + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + @@ -1167,6 +1404,30 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + + + + @@ -1205,12 +1466,35 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -8943,7 +9263,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -9165,7 +9485,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z has small molecule regulator @@ -9178,7 +9498,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z has small molecule activator @@ -9191,7 +9511,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z has small molecule inhibitor @@ -9203,7 +9523,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z @@ -9218,7 +9538,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z is small molecule regulator of @@ -9231,9 +9551,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -9244,9 +9565,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -9256,7 +9578,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z results in adhesion of @@ -9267,7 +9589,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z @@ -9282,11 +9604,12 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -9296,11 +9619,12 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z removes input for + https://wiki.geneontology.org/Removes_input_for @@ -9310,7 +9634,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -9323,7 +9647,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -9339,7 +9663,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -9357,7 +9681,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z receives synaptic input in region @@ -9374,7 +9698,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z sends synaptic output to region @@ -9386,7 +9710,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z has synaptic IO throughout @@ -9399,7 +9723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z receives synaptic input throughout @@ -9412,7 +9736,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z sends synaptic output throughout @@ -9428,7 +9752,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -9444,7 +9768,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z receives synaptic input from neuron @@ -9456,7 +9780,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. sends synaptic output to cell @@ -9469,7 +9793,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + disease has infectious agent @@ -9524,7 +9848,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. - + has marker gene combination has marker signature set has characterizing marker set @@ -9642,8 +9966,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + has high plasma membrane amount @@ -9661,8 +9985,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + has low plasma membrane amount @@ -9678,8 +10002,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z has phenotype or disease https://github.com/oborel/obo-relations/issues/478 @@ -9691,8 +10015,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -9705,8 +10029,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z has exposure medium @@ -9732,6 +10056,34 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relation between entities in which one increases or decreases as the other does the same. + directly correlated with + + positively correlated with + + + + + + + + + + + A relation between entities in which one increases as the other decreases. + inversely correlated with + + negatively correlated with + + + + @@ -9777,7 +10129,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + is agonist of @@ -9790,7 +10142,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + is inverse agonist of @@ -9803,13 +10155,243 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + is antagonist of + + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical. + + chemical relationship + + + + + + + + + + pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) + A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B. + + + is direct conjugate base of + + + + + + + + + + neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) + A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B. + + + is direct conjugate acid of + + + + + + + + + + + + (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. + A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_base_of + is deprotonated form of + + + + + + + + + + + (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. + A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_acid_of + is protonated form of + + + + + + + + + + + phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol. + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + 2023-02-28T18:53:32Z + is MMP with + is matched molecular pair with + is matched small molecular pair with + + + + + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + + + + + + + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + Two chemicals are tautomers if they can be readily interconverted. + +This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms. + + 2023-03-18T23:49:31Z + obo:chebi#is_tautomer_of + is desmotrope of + is tautomer of + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + + + + + + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. + + 2023-03-18T23:49:31Z + obo:chebi#is_substituent_group_from + is substitutent group from + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + + + + + + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. + +For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship. + + 2023-03-18T23:49:31Z + obo:chebi#has_functional_parent + has functional parent + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + + + + + + + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. + +A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers). + + 2023-03-18T23:49:31Z + obo:chebi#is_enantiomer_of + is optical isomer of + is enantiomer of + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + + + + + + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. + + 2023-03-18T23:49:31Z + obo:chebi#has_parent_hydride + has parent hydride + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + + + + + + @@ -9864,7 +10446,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + confers susceptibility to condition @@ -11531,7 +12113,7 @@ For example, protein A (transcription factor) indirectly increases by expression Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - dos + 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate @@ -11557,50 +12139,146 @@ For example, protein A (transcription factor) indirectly increases by expression - + - - ## Elucidation + + example to be eventually removed + example to be eventually removed + + -This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; -## How to interpret (informal) + -First the &quot;atemporal&quot; FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + -## Example - Class: nucleus - SubClassOf: part_of some cell + - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + -## Notes -This interpretation is *not* the same as an at-all-times relation - axiom holds for all times + + + + ready for release + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release - + - - ## Elucidation + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. -## Example: + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + pending final vetting + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + requires discussion + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm @@ -11617,6 +12295,279 @@ binary, and takes no temporal argument. + + + + Researcher + Austin Meier + + + + + Researcher + + + + + + Austin Meier + + + + + + + + + researcher + Shawn Zheng Kai Tan + + + + + researcher + + + + + + Shawn Zheng Kai Tan + + + + + + + + + researcher, metadata, diseases, University of Maryland + Lynn Schriml + + + + + researcher, metadata, diseases, University of Maryland + + + + + + Lynn Schriml + + + + + + + + + data scientist + Anne Thessen + + + + + data scientist + + + + + + Anne Thessen + + + + + + + + + researcher + Pier Luigi Buttigieg + + + + + researcher + + + + + + Pier Luigi Buttigieg + + + + + + + + + bioinformatics researcher + Christopher J. Mungall + + + + + bioinformatics researcher + + + + + + Christopher J. Mungall + + + + + + + + + researcher + David Osumi-Sutherland + + + + + researcher + + + + + + David Osumi-Sutherland + + + + + + + + + researcher + Lauren E. Chan + + + + + researcher + + + + + + Lauren E. Chan + + + + + + + + + researcher + Marie-Angélique Laporte + + + + + researcher + + + + + + Marie-Angélique Laporte + + + + + + + + + researcher + James P. Balhoff + + + + + researcher + + + + + + James P. Balhoff + + + + + + + + + researcher + Lindsay G Cowell + + + + + researcher + + + + + + Lindsay G Cowell + + + + + + + + + researcher + Anna Maria Masci + + + + + researcher + + + + + + Anna Maria Masci + + + + + + + + + American chemist + Charles Tapley Hoyt + + + + + American chemist + + + + + + Charles Tapley Hoyt + + + + + - - - curation status specification + + data item + data item - - - ready for release + + data about an ontology part + Data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part - - - pending final vetting + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolete_core + obsolescence reason specification + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot obsolescence reason specification - + + placeholder removed + placeholder removed + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + ontology term requester - requires discussion + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + denotator type + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + is denotator type + Relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + antisymmetric property + part_of antisymmetric property xsd:true + Use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + has ID digit count + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + has ID range allocated + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + has ID policy for + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + has ID prefix + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + has associated axiom(nl) + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + has associated axiom(fol) + + + is allocated id range + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + Add as annotation triples in the granting ontology + is allocated id range + + + may be identical to + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + scheduled for obsoletion on or after + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + scheduled for obsoletion on or after + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + has axiom label + + + ontology module + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module + + + base ontology module + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + base ontology module + + + + editors ontology module + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + editors ontology module + + + main release ontology module + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + main release ontology module + + + bridge ontology module + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + bridge ontology module + + + + import ontology module + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + import ontology module + + + + subset ontology module + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + subset ontology module + + + + + curation subset ontology module + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + curation subset ontology module + + + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module + + + single layer ontology module + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + single layer subset ontology module + + + exclusion subset ontology module + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + exclusion subset ontology module + + + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module + + + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module + + + + reasoned ontology module + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + reasoned ontology module + + + + generated ontology module + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + generated ontology module + + + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module + + + + + + taxonomic bridge ontology module + taxonomic bridge ontology module + + + ontology module subsetted by expressivity + ontology module subsetted by expressivity + + + obo basic subset ontology module + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + obo basic subset ontology module + + + + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile + + + EL++ ontology module + EL++ ontology module + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + out of scope + + + This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. + OBO Operations call + + logical characteristic of object property + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initalisms + + abbreviation + + + A synonym type for describing ambiguous synonyms + + ambiguous synonym + + + A synonym type for describing dubious synonyms + + dubious synonym + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + layperson synonym + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + plural form + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + UK spelling synonym + + + A synonym type for common misspellings + + misspelling + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + misnomer + + + + + + + + + + + + + + + + + + @@ -11668,13 +13022,13 @@ binary, and takes no temporal argument. - + - + - + @@ -11686,13 +13040,16 @@ binary, and takes no temporal argument. + + + - + @@ -11701,9 +13058,6 @@ binary, and takes no temporal argument. - - - @@ -11891,9 +13245,9 @@ binary, and takes no temporal argument. - - - + + + @@ -11902,9 +13256,9 @@ binary, and takes no temporal argument. - - - + + + @@ -11936,9 +13290,9 @@ binary, and takes no temporal argument. - + - + @@ -11947,9 +13301,9 @@ binary, and takes no temporal argument. - + - + @@ -11981,9 +13335,9 @@ binary, and takes no temporal argument. - + - + @@ -11992,9 +13346,9 @@ binary, and takes no temporal argument. - + - + @@ -12026,9 +13380,9 @@ binary, and takes no temporal argument. - + - + @@ -12037,9 +13391,9 @@ binary, and takes no temporal argument. - + - + @@ -12071,9 +13425,9 @@ binary, and takes no temporal argument. - + - + @@ -12082,9 +13436,9 @@ binary, and takes no temporal argument. - + - + @@ -12115,7 +13469,7 @@ binary, and takes no temporal argument. - + @@ -12126,7 +13480,7 @@ binary, and takes no temporal argument. - + @@ -12159,9 +13513,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12170,9 +13524,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12203,9 +13557,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12214,9 +13568,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12247,9 +13601,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12258,9 +13612,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12291,9 +13645,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12302,9 +13656,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12336,8 +13690,8 @@ binary, and takes no temporal argument. - - + + @@ -12347,8 +13701,8 @@ binary, and takes no temporal argument. - - + + diff --git a/src/ontology/subsets/ro-developmental.json b/src/ontology/subsets/ro-developmental.json index 4c466e7e..3962522d 100644 --- a/src/ontology/subsets/ro-developmental.json +++ b/src/ontology/subsets/ro-developmental.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index f8e39bda..9dcabaf6 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index a7ea63b4..4276963b 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-developmental.tsv b/src/ontology/subsets/ro-developmental.tsv index 72cdad17..87b847f2 100644 --- a/src/ontology/subsets/ro-developmental.tsv +++ b/src/ontology/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid1 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid18 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid22 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid26 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid33 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid37 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid40 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid5 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid52 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid58 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid61 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid64 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid67 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid9 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid1 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid18 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid22 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid26 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid33 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid37 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid40 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid5 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid52 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid58 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid61 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid64 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid67 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid9 @@ -26,19 +26,14 @@ _:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid9 + + + + + + diff --git a/src/ontology/subsets/ro-hom.json b/src/ontology/subsets/ro-hom.json index ade7fe10..b36f3b6d 100644 --- a/src/ontology/subsets/ro-hom.json +++ b/src/ontology/subsets/ro-hom.json @@ -2802,7 +2802,7 @@ } ], "domainRangeAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] } ] } ] } \ No newline at end of file diff --git a/src/ontology/subsets/ro-hom.obo b/src/ontology/subsets/ro-hom.obo index 27d2a0be..1a6836f2 100644 --- a/src/ontology/subsets/ro-hom.obo +++ b/src/ontology/subsets/ro-hom.obo @@ -952,7 +952,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -range: CARO:0001010 +range: OBI:0100026 is_a: evolutionarily_related_to ! evolutionarily related to [Typedef] diff --git a/src/ontology/subsets/ro-hom.owl b/src/ontology/subsets/ro-hom.owl index 3a039acb..48b144e7 100644 --- a/src/ontology/subsets/ro-hom.owl +++ b/src/ontology/subsets/ro-hom.owl @@ -225,7 +225,7 @@ - + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. @@ -2035,9 +2035,9 @@ - + - + diff --git a/src/ontology/subsets/ro-hom.tsv b/src/ontology/subsets/ro-hom.tsv index 9e64d1bd..2763a43a 100644 --- a/src/ontology/subsets/ro-hom.tsv +++ b/src/ontology/subsets/ro-hom.tsv @@ -1,2 +1,2 @@ ?x ?label - + diff --git a/src/ontology/subsets/ro-interaction.json b/src/ontology/subsets/ro-interaction.json index 67569205..4a01601a 100644 --- a/src/ontology/subsets/ro-interaction.json +++ b/src/ontology/subsets/ro-interaction.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index 57efd25a..d0b641be 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index 4a151349..b9a16f07 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-interaction.tsv b/src/ontology/subsets/ro-interaction.tsv index 3cfed9ea..a67d022a 100644 --- a/src/ontology/subsets/ro-interaction.tsv +++ b/src/ontology/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid1 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid18 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid22 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid26 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid33 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid37 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid40 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid5 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid52 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid58 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid61 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid64 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid67 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid9 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid1 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid18 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid22 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid26 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid33 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid37 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid40 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid5 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid52 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid58 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid61 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid64 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid67 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid9 @@ -26,19 +26,14 @@ _:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid9 + + + + + + diff --git a/src/ontology/subsets/ro-mereotopology.json b/src/ontology/subsets/ro-mereotopology.json index 2e50b0cc..080ee607 100644 --- a/src/ontology/subsets/ro-mereotopology.json +++ b/src/ontology/subsets/ro-mereotopology.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index ba745b5e..f034bad4 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 6b552729..14422f3a 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-mereotopology.tsv b/src/ontology/subsets/ro-mereotopology.tsv index 22ae47d4..54a82ec4 100644 --- a/src/ontology/subsets/ro-mereotopology.tsv +++ b/src/ontology/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid1 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid18 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid22 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid26 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid33 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid37 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid40 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid5 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid52 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid58 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid61 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid64 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid67 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid9 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid1 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid18 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid22 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid26 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid33 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid37 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid40 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid5 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid52 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid58 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid61 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid64 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid67 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid9 @@ -26,19 +26,14 @@ _:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid9 + + + + + + diff --git a/src/ontology/subsets/ro-sequence.json b/src/ontology/subsets/ro-sequence.json index 3d3191dc..668e1a01 100644 --- a/src/ontology/subsets/ro-sequence.json +++ b/src/ontology/subsets/ro-sequence.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index fde68107..6f5694a7 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index 4482b19b..e8536f0f 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-sequence.tsv b/src/ontology/subsets/ro-sequence.tsv index 26716d47..c1f7657a 100644 --- a/src/ontology/subsets/ro-sequence.tsv +++ b/src/ontology/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid1 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid18 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid22 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid26 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid33 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid37 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid40 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid5 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid52 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid58 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid61 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid64 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid67 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid9 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid1 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid18 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid22 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid26 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid33 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid37 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid40 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid5 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid52 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid58 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid61 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid64 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid67 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid9 @@ -26,19 +26,14 @@ _:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid9 + + + + + + diff --git a/src/ontology/subsets/ro-time-interval.json b/src/ontology/subsets/ro-time-interval.json index 47bf0880..a5d73b5b 100644 --- a/src/ontology/subsets/ro-time-interval.json +++ b/src/ontology/subsets/ro-time-interval.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 8150a607..3517257d 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 286fb05e..d131f24e 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-time-interval.tsv b/src/ontology/subsets/ro-time-interval.tsv index 8eb702f1..406af670 100644 --- a/src/ontology/subsets/ro-time-interval.tsv +++ b/src/ontology/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid1 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid18 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid22 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid26 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid33 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid37 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid40 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid5 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid52 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid58 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid61 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid64 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid67 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid9 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid1 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid18 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid22 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid26 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid33 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid37 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid40 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid5 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid52 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid58 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid61 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid64 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid67 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid9 @@ -26,19 +26,14 @@ _:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid9 + + + + + + diff --git a/subsets/ro-causal.json b/subsets/ro-causal.json index 7e8d7fb2..8b89b440 100644 --- a/subsets/ro-causal.json +++ b/subsets/ro-causal.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 87ecf23c..942e3a70 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index bada75b7..716fd015 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-causal.tsv b/subsets/ro-causal.tsv index 49389a06..b039df98 100644 --- a/subsets/ro-causal.tsv +++ b/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid1 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid18 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid22 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid26 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid33 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid37 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid40 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid5 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid52 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid58 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid61 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid64 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid67 -_:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid9 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid1 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid18 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid22 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid26 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid33 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid37 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid40 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid5 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid52 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid58 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid61 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid64 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid67 +_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid9 @@ -26,19 +26,14 @@ _:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B7386935aX2D2e60X2D44ceX2Dae14X2D1be5205b6c44genid9 + + + + + + diff --git a/subsets/ro-chado.json b/subsets/ro-chado.json index 93184cd1..f86a1d5d 100644 --- a/subsets/ro-chado.json +++ b/subsets/ro-chado.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-02-22" + "val" : "2023-06-28" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-22/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -74,6 +74,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -181,173 +184,1443 @@ "deprecated" : true } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occurs_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", + "lbl" : "derives from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example to be eventually removed" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "lbl" : "data item", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data item" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "lbl" : "data about an ontology part", + "meta" : { + "definition" : { + "val" : "Data about an ontology part is a data item about a part of an ontology, for example a term" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data about an ontology part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "failed exploratory term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "lbl" : "editor preferred term", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl" : "example of usage", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example of usage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "lbl" : "in branch", + "meta" : { + "definition" : { + "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "in branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "lbl" : "has curation status", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has curation status" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "lbl" : "term editor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term editor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "lbl" : "alternative label", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like." + }, + "comments" : [ "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "OBO Operations committee" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "lbl" : "definition source", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition source" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "metadata complete" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "organizational term" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ready for release" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "metadata incomplete" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "uncurated" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "pending final vetting" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000224", + "lbl" : "obsolete_core", + "meta" : { + "definition" : { + "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl" : "obsolescence reason specification", + "meta" : { + "definition" : { + "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obsolescence reason specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "placeholder removed" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "terms merged" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term imported" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term split" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has obsolescence reason" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "lbl" : "curator note", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An administrative note of use for a curator but of no use for a user" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curator note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." + }, + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "lbl" : "ontology term requester", + "meta" : { + "definition" : { + "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition." + }, + "comments" : [ "The 'term requester' can credit the person, organization or project who request the ontology term." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology term requester" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "lbl" : "denotator type", + "meta" : { + "definition" : { + "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "universal" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "lbl" : "is denotator type", + "meta" : { + "definition" : { + "val" : "Relates an class defined in an ontology, to the type of it's denotator" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "lbl" : "imported from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "For external terms/classes, the ontology from which the term was imported" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "imported from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "meta" : { + "definition" : { + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "defined class" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "meta" : { + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "named class expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "to be replaced with external ontology term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand expression to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "lbl" : "expand assertion to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand assertion to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "lbl" : "first order logic expression", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "first order logic expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "lbl" : "antisymmetric property", + "meta" : { + "definition" : { + "val" : "Use boolean value xsd:true to indicate that the property is an antisymmetric property" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "antisymmetric property" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part_of antisymmetric property xsd:true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "requires discussion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl" : "OBO foundry unique label", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which is unique across the OBO Foundry." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "OBO foundry unique label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBO Foundry " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "lbl" : "has ID digit count", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID digit count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "lbl" : "has ID range allocated to", + "meta" : { + "definition" : { + "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID range allocated" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "lbl" : "has ID policy for", + "meta" : { + "definition" : { + "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID policy for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "lbl" : "has ID prefix", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ID prefix" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl" : "elucidation", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "elucidation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Barry Smith" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "lbl" : "has associated axiom(nl)", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(nl)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom associated with a term expressed using natural language" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "lbl" : "has associated axiom(fol)", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(fol)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom expressed in first order logic using CLIF syntax" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "lbl" : "is allocated id range", + "meta" : { + "definition" : { + "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is allocated id range" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "has ontology root term", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ontology root term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Nicolas Matentzoglu" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "lbl" : "may be identical to", + "meta" : { + "definition" : { + "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged." + }, + "comments" : [ "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "may be identical to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "lbl" : "scheduled for obsoletion on or after", + "meta" : { + "definition" : { + "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "scheduled for obsoletion on or after" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall, Jie Zheng" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "lbl" : "has axiom label", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has axiom id" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term replaced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "lbl" : "ontology module", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology file" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "lbl" : "base ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "base ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "lbl" : "editors ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editors ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "lbl" : "main release ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "main release ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "lbl" : "bridge ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bridge ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000005", + "lbl" : "import ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology module that is intended to be imported from another ontology." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "import ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add axioms that indicate this is the output of a module extraction process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "import file" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/extract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000006", + "lbl" : "subset ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology slim" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "subset ontology" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/filter" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000007", + "lbl" : "curation subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation subset ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000008", + "lbl" : "analysis subset ontology module", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended for usage in analysis or discovery applications." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "analysis ontology module" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000009", + "lbl" : "single layer subset ontology module", "meta" : { "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" + "val" : "single layer ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + "val" : "ribbon subset" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "lbl" : "exclusion subset ontology module", "meta" : { "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" + "val" : "exclusion subset ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "lbl" : "external import ontology module", "meta" : { "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" + "val" : "external import ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" + "val" : "external import" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "lbl" : "species subset ontology module", + "meta" : { + "definition" : { + "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "species subset ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" + "val" : "taxon subset" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "lbl" : "reasoned ontology module", "meta" : { "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" + "val" : "reasoned ontology module" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", - "lbl" : "derives from part of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "lbl" : "generated ontology module", "meta" : { "definition" : { - "val" : "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." - } + "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "generated ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000078", - "lbl" : "curation status specification", + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "lbl" : "template generated ontology module", "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "template generated ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "lbl" : "taxonomic bridge ontology module", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "taxonomic bridge ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "lbl" : "ontology module subsetted by expressivity", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module subsetted by expressivity" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000225", - "lbl" : "obsolescence reason specification", + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "lbl" : "obo basic subset ontology module", "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obo basic subset ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000426", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "lbl" : "ontology module subsetted by OWL profile", "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." - } + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "ontology module subsetted by OWL profile" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "lbl" : "EL++ ontology module", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "EL++ ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000589", - "lbl" : "OBO foundry unique label", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", "meta" : { + "definition" : { + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/OMO_0001001", + "lbl" : "logical characteristic of object property", "meta" : { + "definition" : { + "val" : "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBO Operations call" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -361,6 +1634,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : - - 2023-02-22 + + 2023-06-28 @@ -45,82 +46,211 @@ - + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + editor preferred term + - + + example of usage + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage + example of usage + - + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + has curation status + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition + definition - + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + editor note + - + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + term editor + - + + alternative label + + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label + - + + definition source + + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source + - + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + - + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from + - + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + - + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + first order logic expression An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + PERSON:Alan Ruttenberg + first order logic expression @@ -129,7 +259,15 @@ + OBO foundry unique label + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label @@ -137,20 +275,36 @@ - + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + elucidation + - + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + + term replaced by + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by @@ -178,6 +332,7 @@ ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + defined by construct @@ -845,7 +1000,7 @@ Where we have an annotation assertion true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - + nominally disjoint with @@ -904,7 +1059,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:29Z valid_for_go_annotation_extension @@ -916,7 +1071,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:18Z valid_for_go_gp2term @@ -928,7 +1083,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:04:12Z valid_for_go_ontology @@ -940,7 +1095,7 @@ Where we have an annotation assertion - pg + 2020-09-22T11:05:45Z valid_for_gocam @@ -959,6 +1114,22 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + @@ -983,18 +1154,36 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + @@ -1019,12 +1208,24 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -1061,12 +1262,24 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -1102,7 +1315,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym has_broad_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + @@ -1118,7 +1337,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym has_exact_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + @@ -1126,7 +1351,13 @@ Where we have an annotation assertion + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym has_narrow_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + @@ -1142,7 +1373,13 @@ Where we have an annotation assertion + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym has_related_synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + @@ -1167,6 +1404,30 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + + + + @@ -1205,12 +1466,35 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -8943,7 +9263,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -9165,7 +9485,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z has small molecule regulator @@ -9178,7 +9498,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z has small molecule activator @@ -9191,7 +9511,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z has small molecule inhibitor @@ -9203,7 +9523,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z @@ -9218,7 +9538,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z is small molecule regulator of @@ -9231,9 +9551,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -9244,9 +9565,10 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -9256,7 +9578,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z results in adhesion of @@ -9267,7 +9589,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z @@ -9282,11 +9604,12 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -9296,11 +9619,12 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z removes input for + https://wiki.geneontology.org/Removes_input_for @@ -9310,7 +9634,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -9323,7 +9647,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -9339,7 +9663,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -9357,7 +9681,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z receives synaptic input in region @@ -9374,7 +9698,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z sends synaptic output to region @@ -9386,7 +9710,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z has synaptic IO throughout @@ -9399,7 +9723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z receives synaptic input throughout @@ -9412,7 +9736,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z sends synaptic output throughout @@ -9428,7 +9752,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -9444,7 +9768,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z receives synaptic input from neuron @@ -9456,7 +9780,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. sends synaptic output to cell @@ -9469,7 +9793,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + disease has infectious agent @@ -9524,7 +9848,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. - + has marker gene combination has marker signature set has characterizing marker set @@ -9642,8 +9966,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + has high plasma membrane amount @@ -9661,8 +9985,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + has low plasma membrane amount @@ -9678,8 +10002,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z has phenotype or disease https://github.com/oborel/obo-relations/issues/478 @@ -9691,8 +10015,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -9705,8 +10029,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z has exposure medium @@ -9732,6 +10056,34 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relation between entities in which one increases or decreases as the other does the same. + directly correlated with + + positively correlated with + + + + + + + + + + + A relation between entities in which one increases as the other decreases. + inversely correlated with + + negatively correlated with + + + + @@ -9777,7 +10129,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + is agonist of @@ -9790,7 +10142,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + is inverse agonist of @@ -9803,13 +10155,243 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + is antagonist of + + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical. + + chemical relationship + + + + + + + + + + pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) + A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B. + + + is direct conjugate base of + + + + + + + + + + neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) + A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B. + + + is direct conjugate acid of + + + + + + + + + + + + (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. + A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_base_of + is deprotonated form of + + + + + + + + + + + (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. + A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. + +This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. + + obo:chebi#is_conjugate_acid_of + is protonated form of + + + + + + + + + + + phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol. + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + 2023-02-28T18:53:32Z + is MMP with + is matched molecular pair with + is matched small molecular pair with + + + + + A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. + +While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. + +This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. + +This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. + + + + + + + + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + Two chemicals are tautomers if they can be readily interconverted. + +This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms. + + 2023-03-18T23:49:31Z + obo:chebi#is_tautomer_of + is desmotrope of + is tautomer of + + + + + + 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. + + + + + + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. + + 2023-03-18T23:49:31Z + obo:chebi#is_substituent_group_from + is substitutent group from + + + + + + carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) + + + + + + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. + +For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship. + + 2023-03-18T23:49:31Z + obo:chebi#has_functional_parent + has functional parent + + + + + + hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) + + + + + + + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. + +A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers). + + 2023-03-18T23:49:31Z + obo:chebi#is_enantiomer_of + is optical isomer of + is enantiomer of + + + + + + dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. + + + + + + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. + + 2023-03-18T23:49:31Z + obo:chebi#has_parent_hydride + has parent hydride + + + + + + pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. + + + + + + @@ -9864,7 +10446,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + confers susceptibility to condition @@ -11531,7 +12113,7 @@ For example, protein A (transcription factor) indirectly increases by expression Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - dos + 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate @@ -11557,50 +12139,146 @@ For example, protein A (transcription factor) indirectly increases by expression - + - - ## Elucidation + + example to be eventually removed + example to be eventually removed + + -This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; -## How to interpret (informal) + -First the &quot;atemporal&quot; FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + -## Example - Class: nucleus - SubClassOf: part_of some cell + - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + -## Notes -This interpretation is *not* the same as an at-all-times relation - axiom holds for all times + + + + ready for release + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release - + - - ## Elucidation + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. -## Example: + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + pending final vetting + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + requires discussion + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm @@ -11617,6 +12295,279 @@ binary, and takes no temporal argument. + + + + Researcher + Austin Meier + + + + + Researcher + + + + + + Austin Meier + + + + + + + + + researcher + Shawn Zheng Kai Tan + + + + + researcher + + + + + + Shawn Zheng Kai Tan + + + + + + + + + researcher, metadata, diseases, University of Maryland + Lynn Schriml + + + + + researcher, metadata, diseases, University of Maryland + + + + + + Lynn Schriml + + + + + + + + + data scientist + Anne Thessen + + + + + data scientist + + + + + + Anne Thessen + + + + + + + + + researcher + Pier Luigi Buttigieg + + + + + researcher + + + + + + Pier Luigi Buttigieg + + + + + + + + + bioinformatics researcher + Christopher J. Mungall + + + + + bioinformatics researcher + + + + + + Christopher J. Mungall + + + + + + + + + researcher + David Osumi-Sutherland + + + + + researcher + + + + + + David Osumi-Sutherland + + + + + + + + + researcher + Lauren E. Chan + + + + + researcher + + + + + + Lauren E. Chan + + + + + + + + + researcher + Marie-Angélique Laporte + + + + + researcher + + + + + + Marie-Angélique Laporte + + + + + + + + + researcher + James P. Balhoff + + + + + researcher + + + + + + James P. Balhoff + + + + + + + + + researcher + Lindsay G Cowell + + + + + researcher + + + + + + Lindsay G Cowell + + + + + + + + + researcher + Anna Maria Masci + + + + + researcher + + + + + + Anna Maria Masci + + + + + + + + + American chemist + Charles Tapley Hoyt + + + + + American chemist + + + + + + Charles Tapley Hoyt + + + + + - - - curation status specification + + data item + data item - - - ready for release + + data about an ontology part + Data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part - - - pending final vetting + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolete_core + obsolescence reason specification + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot obsolescence reason specification - + + placeholder removed + placeholder removed + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + ontology term requester - requires discussion + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + denotator type + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + is denotator type + Relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + antisymmetric property + part_of antisymmetric property xsd:true + Use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + has ID digit count + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + has ID range allocated + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + has ID policy for + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + has ID prefix + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + has associated axiom(nl) + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + has associated axiom(fol) + + + is allocated id range + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + Add as annotation triples in the granting ontology + is allocated id range + + + may be identical to + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + scheduled for obsoletion on or after + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + scheduled for obsoletion on or after + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + has axiom label + + + ontology module + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module + + + base ontology module + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + base ontology module + + + + editors ontology module + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + editors ontology module + + + main release ontology module + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + main release ontology module + + + bridge ontology module + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + bridge ontology module + + + + import ontology module + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + import ontology module + + + + subset ontology module + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + subset ontology module + + + + + curation subset ontology module + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + curation subset ontology module + + + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module + + + single layer ontology module + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + single layer subset ontology module + + + exclusion subset ontology module + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + exclusion subset ontology module + + + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module + + + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module + + + + reasoned ontology module + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + reasoned ontology module + + + + generated ontology module + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + generated ontology module + + + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module + + + + + + taxonomic bridge ontology module + taxonomic bridge ontology module + + + ontology module subsetted by expressivity + ontology module subsetted by expressivity + + + obo basic subset ontology module + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + obo basic subset ontology module + + + + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile + + + EL++ ontology module + EL++ ontology module + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + out of scope + + + This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. + OBO Operations call + + logical characteristic of object property + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initalisms + + abbreviation + + + A synonym type for describing ambiguous synonyms + + ambiguous synonym + + + A synonym type for describing dubious synonyms + + dubious synonym + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + layperson synonym + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + plural form + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + UK spelling synonym + + + A synonym type for common misspellings + + misspelling + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + misnomer + + + + + + + + + + + + + + + + + + @@ -11668,13 +13022,13 @@ binary, and takes no temporal argument. - + - + - + @@ -11686,13 +13040,16 @@ binary, and takes no temporal argument. + + + - + @@ -11701,9 +13058,6 @@ binary, and takes no temporal argument. - - - @@ -11891,9 +13245,9 @@ binary, and takes no temporal argument. - - - + + + @@ -11902,9 +13256,9 @@ binary, and takes no temporal argument. - - - + + + @@ -11936,9 +13290,9 @@ binary, and takes no temporal argument. - + - + @@ -11947,9 +13301,9 @@ binary, and takes no temporal argument. - + - + @@ -11981,9 +13335,9 @@ binary, and takes no temporal argument. - + - + @@ -11992,9 +13346,9 @@ binary, and takes no temporal argument. - + - + @@ -12026,9 +13380,9 @@ binary, and takes no temporal argument. - + - + @@ -12037,9 +13391,9 @@ binary, and takes no temporal argument. - + - + @@ -12071,9 +13425,9 @@ binary, and takes no temporal argument. - + - + @@ -12082,9 +13436,9 @@ binary, and takes no temporal argument. - + - + @@ -12115,7 +13469,7 @@ binary, and takes no temporal argument. - + @@ -12126,7 +13480,7 @@ binary, and takes no temporal argument. - + @@ -12159,9 +13513,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12170,9 +13524,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12203,9 +13557,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12214,9 +13568,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12247,9 +13601,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12258,9 +13612,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12291,9 +13645,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12302,9 +13656,9 @@ binary, and takes no temporal argument. - - - + + + @@ -12336,8 +13690,8 @@ binary, and takes no temporal argument. - - + + @@ -12347,8 +13701,8 @@ binary, and takes no temporal argument. - - + + diff --git a/subsets/ro-developmental.json b/subsets/ro-developmental.json index 4c466e7e..3962522d 100644 --- a/subsets/ro-developmental.json +++ b/subsets/ro-developmental.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index f8e39bda..9dcabaf6 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index a7ea63b4..4276963b 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-developmental.tsv b/subsets/ro-developmental.tsv index 72cdad17..87b847f2 100644 --- a/subsets/ro-developmental.tsv +++ b/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid1 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid18 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid22 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid26 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid33 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid37 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid40 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid5 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid52 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid58 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid61 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid64 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid67 -_:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid9 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid1 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid18 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid22 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid26 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid33 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid37 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid40 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid5 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid52 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid58 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid61 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid64 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid67 +_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid9 @@ -26,19 +26,14 @@ _:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B7446b81fX2Db81fX2D4d83X2D9f42X2D6ea71e3b666fgenid9 + + + + + + diff --git a/subsets/ro-hom.json b/subsets/ro-hom.json index ade7fe10..b36f3b6d 100644 --- a/subsets/ro-hom.json +++ b/subsets/ro-hom.json @@ -2802,7 +2802,7 @@ } ], "domainRangeAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] } ] } ] } \ No newline at end of file diff --git a/subsets/ro-hom.obo b/subsets/ro-hom.obo index 27d2a0be..1a6836f2 100644 --- a/subsets/ro-hom.obo +++ b/subsets/ro-hom.obo @@ -952,7 +952,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -range: CARO:0001010 +range: OBI:0100026 is_a: evolutionarily_related_to ! evolutionarily related to [Typedef] diff --git a/subsets/ro-hom.owl b/subsets/ro-hom.owl index 3a039acb..48b144e7 100644 --- a/subsets/ro-hom.owl +++ b/subsets/ro-hom.owl @@ -225,7 +225,7 @@ - + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. @@ -2035,9 +2035,9 @@ - + - + diff --git a/subsets/ro-hom.tsv b/subsets/ro-hom.tsv index 9e64d1bd..2763a43a 100644 --- a/subsets/ro-hom.tsv +++ b/subsets/ro-hom.tsv @@ -1,2 +1,2 @@ ?x ?label - + diff --git a/subsets/ro-interaction.json b/subsets/ro-interaction.json index 67569205..4a01601a 100644 --- a/subsets/ro-interaction.json +++ b/subsets/ro-interaction.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index 57efd25a..d0b641be 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index 4a151349..b9a16f07 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-interaction.tsv b/subsets/ro-interaction.tsv index 3cfed9ea..a67d022a 100644 --- a/subsets/ro-interaction.tsv +++ b/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid1 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid18 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid22 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid26 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid33 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid37 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid40 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid5 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid52 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid58 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid61 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid64 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid67 -_:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid9 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid1 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid18 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid22 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid26 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid33 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid37 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid40 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid5 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid52 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid58 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid61 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid64 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid67 +_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid9 @@ -26,19 +26,14 @@ _:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B144ecc17X2Da886X2D49e2X2Dad46X2D42891e404317genid9 + + + + + + diff --git a/subsets/ro-mereotopology.json b/subsets/ro-mereotopology.json index 2e50b0cc..080ee607 100644 --- a/subsets/ro-mereotopology.json +++ b/subsets/ro-mereotopology.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index ba745b5e..f034bad4 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 6b552729..14422f3a 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-mereotopology.tsv b/subsets/ro-mereotopology.tsv index 22ae47d4..54a82ec4 100644 --- a/subsets/ro-mereotopology.tsv +++ b/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid1 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid18 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid22 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid26 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid33 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid37 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid40 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid5 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid52 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid58 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid61 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid64 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid67 -_:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid9 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid1 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid18 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid22 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid26 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid33 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid37 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid40 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid5 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid52 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid58 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid61 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid64 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid67 +_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid9 @@ -26,19 +26,14 @@ _:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:Bb44351c2X2Da2a0X2D4b2fX2Db086X2D3adb068f56a9genid9 + + + + + + diff --git a/subsets/ro-sequence.json b/subsets/ro-sequence.json index 3d3191dc..668e1a01 100644 --- a/subsets/ro-sequence.json +++ b/subsets/ro-sequence.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index fde68107..6f5694a7 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index 4482b19b..e8536f0f 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-sequence.tsv b/subsets/ro-sequence.tsv index 26716d47..c1f7657a 100644 --- a/subsets/ro-sequence.tsv +++ b/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid1 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid18 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid22 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid26 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid33 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid37 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid40 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid5 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid52 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid58 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid61 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid64 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid67 -_:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid9 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid1 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid18 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid22 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid26 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid33 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid37 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid40 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid5 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid52 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid58 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid61 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid64 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid67 +_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid9 @@ -26,19 +26,14 @@ _:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B717a7b44X2D2243X2D4da2X2D8d82X2Da9f11d85112agenid9 + + + + + + diff --git a/subsets/ro-time-interval.json b/subsets/ro-time-interval.json index 47bf0880..a5d73b5b 100644 --- a/subsets/ro-time-interval.json +++ b/subsets/ro-time-interval.json @@ -73,6 +73,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -788,7 +791,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -811,7 +814,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -834,7 +837,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -854,7 +857,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:36:08Z" @@ -874,7 +877,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -896,7 +899,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -918,7 +921,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-19T17:30:36Z" @@ -940,7 +943,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:11:08Z" @@ -962,7 +965,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" @@ -982,7 +985,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -998,14 +1001,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002023" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -1021,14 +1024,14 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002024" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -1044,7 +1047,7 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "xrefs" : [ { @@ -1052,7 +1055,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -1068,14 +1071,14 @@ "meta" : { "definition" : { "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "xrefs" : [ { "val" : "RO:0002026" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" @@ -1110,6 +1113,9 @@ "lbl" : "simultaneous with", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + }, "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { @@ -1328,6 +1334,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "happens_during" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Happens_during" } ] } }, { @@ -1360,7 +1369,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "xrefs" : [ { "val" : "RO:0002100" @@ -3032,6 +3041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -3058,6 +3070,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -3550,7 +3565,7 @@ "val" : "acts_upstream_of_or_within" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -3897,6 +3912,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -3920,6 +3938,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -4188,6 +4209,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "contributes_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { @@ -4229,6 +4253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enables" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -4300,7 +4327,7 @@ "val" : "involved_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -4349,6 +4376,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "enabled_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -5381,6 +5411,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -5406,6 +5439,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "indirectly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -5488,9 +5524,6 @@ "val" : "RO:0002413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -5505,6 +5538,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "provides_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { @@ -5682,7 +5718,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -5704,6 +5740,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_active_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -7830,7 +7869,7 @@ "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "lumen_of" @@ -8383,6 +8422,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_positively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -8409,6 +8451,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "directly_negatively_regulates" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -8984,7 +9029,7 @@ "meta" : { "definition" : { "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9008,7 +9053,7 @@ "meta" : { "definition" : { "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", - "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "GOC:dph", "GOC:kva", "GOC:pt" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { @@ -9556,7 +9601,7 @@ "val" : "acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9580,6 +9625,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "acts_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9608,7 +9656,7 @@ "val" : "acts_upstream_of,_positive_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -9637,7 +9685,7 @@ "val" : "acts_upstream_of,_negative_effect" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -9660,6 +9708,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -9682,6 +9733,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "causally_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -9820,6 +9874,33 @@ "val" : "has_eggs_laid_on_by" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008509", + "lbl" : "has roost", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0008509" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2908-3327" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-01-18T14:28:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_roost" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -9831,7 +9912,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { "val" : "RO:0009501" @@ -10175,7 +10256,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" @@ -10197,7 +10278,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" @@ -10219,7 +10300,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:54Z" @@ -10242,7 +10323,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" @@ -10264,7 +10345,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" @@ -10286,13 +10367,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_activator_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" } ] } }, { @@ -10308,13 +10392,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "is_small_molecule_inhibitor_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" } ] } }, { @@ -10330,7 +10417,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-08-27T08:13:59Z" @@ -10350,7 +10437,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" @@ -10373,13 +10460,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:01:01Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "constitutively_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Constitutively_upstream_of" } ] } }, { @@ -10396,13 +10486,16 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:06:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "removes_input_for" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Removes_input_for" } ] } }, { @@ -10418,7 +10511,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -10440,7 +10533,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -10466,7 +10559,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" @@ -10488,7 +10581,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" @@ -10510,7 +10603,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" @@ -10532,7 +10625,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" @@ -10554,7 +10647,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" @@ -10576,7 +10669,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" @@ -10608,7 +10701,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" @@ -10630,7 +10723,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" @@ -10653,7 +10746,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" @@ -10675,7 +10768,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "https://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "disease_has_infectious_agent" @@ -10723,10 +10816,10 @@ "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_high_plasma_membrane_amount" @@ -10749,10 +10842,10 @@ "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "val" : "https://orcid.org/0000-0003-1940-6740" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_low_plasma_membrane_amount" @@ -10770,10 +10863,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10795,10 +10888,10 @@ "val" : "RO:0016002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/contributor", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", + "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10823,11 +10916,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2021-12-14T20:41:45Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_exposure_medium" @@ -10889,7 +10982,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10914,7 +11007,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10939,7 +11032,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -11019,7 +11112,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "val" : "https://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "confers_susceptibility_to_condition" @@ -13005,6 +13098,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008509", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0009501", "pred" : "subPropertyOf", @@ -13682,18 +13779,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002101", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] @@ -13708,7 +13805,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002132", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000122" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13718,8 +13815,8 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -13742,7 +13839,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002231", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13763,12 +13860,12 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -13776,10 +13873,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", @@ -13799,18 +13896,18 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001062" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -13872,16 +13969,16 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13891,12 +13988,12 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -13928,7 +14025,7 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], @@ -13946,12 +14043,16 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008509", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000739" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -14029,7 +14130,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] @@ -14050,13 +14151,13 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] } ] } ] } \ No newline at end of file diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 8150a607..3517257d 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -45,7 +45,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -65,7 +65,7 @@ def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004035 property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_negative_effect ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -78,7 +78,7 @@ def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causal subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004034 property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI is_a: acts_upstream_of ! acts upstream of is_a: acts_upstream_of_or_within,_positive_effect ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 @@ -92,7 +92,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] xref: RO:0002264 property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI is_a: causal_agent_in_process ! causal agent in process [Typedef] @@ -101,6 +101,7 @@ name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004033 property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z @@ -111,7 +112,7 @@ name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0004032 property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI is_a: acts_upstream_of_or_within ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z @@ -187,8 +188,8 @@ name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -233,8 +234,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: functionally_related_to ! functionally related to [Typedef] @@ -496,6 +497,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_negative_effect ! causally upstream of or within, negative effect @@ -509,6 +511,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: causally_upstream_of_or_within,_positive_effect ! causally upstream of or within, positive effect @@ -530,6 +533,7 @@ id: causally_upstream_of_or_within,_negative_effect name: causally upstream of or within, negative effect xref: RO:0004046 property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -539,6 +543,7 @@ id: causally_upstream_of_or_within,_positive_effect name: causally upstream of or within, positive effect xref: RO:0004047 property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -728,7 +733,7 @@ name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] xref: RO:0019501 is_a: contributes_to_condition ! contributes to condition -created_by: http://orcid.org/0000-0002-4142-7153 +created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: connected_to @@ -773,8 +778,9 @@ def: "p is constitutively upstream of q iff p is causally upstream of q, p is re subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012009 +property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: causally_upstream_of,_positive_effect ! causally upstream of, positive effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] @@ -804,6 +810,7 @@ property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the in property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: capable_of_part_of ! capable of part of is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of @@ -843,8 +850,8 @@ id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -957,8 +964,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_induces ! developmentally induces @@ -1050,7 +1057,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1096,11 +1103,11 @@ is_a: develops_into ! develops into [Typedef] id: directly_negatively_regulated_by name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002023 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_negatively_regulates ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] @@ -1114,6 +1121,7 @@ xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: negatively_regulates ! negatively regulates @@ -1143,11 +1151,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_positively_regulated_by name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002024 is_a: directly_regulated_by ! directly regulated by inverse_of: directly_positively_regulates ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] @@ -1161,6 +1169,7 @@ xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -1190,11 +1199,11 @@ is_a: directly_regulates_quantity_of ! directly regulates quantity of [Typedef] id: directly_regulated_by name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} xref: RO:0002022 is_a: regulated_by ! regulated by inverse_of: directly_regulates ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] @@ -1238,7 +1247,7 @@ id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] xref: RO:0004030 -range: CARO:0000003 +range: UBERON:0000061 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z @@ -1261,7 +1270,7 @@ name: disease causes dysfunction of xref: RO:0004025 property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 -range: CARO:0000006 +range: UBERON:0000465 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z @@ -1293,7 +1302,7 @@ name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string -range: CARO:0000006 +range: UBERON:0000465 is_a: disease_has_basis_in ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z @@ -1325,7 +1334,7 @@ name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] xref: RO:0014001 is_a: disease_has_basis_in ! disease has basis in -created_by: http://orcid.org/0000-0001-5208-3432 +created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: disease_has_inflammation_site @@ -1439,8 +1448,8 @@ id: ecologically_co-occurs_with name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] xref: RO:0008506 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_symmetric: true is_a: ecologically_related_to ! ecologically related to @@ -1479,6 +1488,7 @@ def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant @@ -1496,6 +1506,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by @@ -1621,7 +1632,7 @@ property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0001001 +range: UBERON:0000122 is_a: overlaps ! overlaps inverse_of: has_fasciculating_neuron_projection ! has fasciculating neuron projection @@ -1677,6 +1688,7 @@ xref: RO:0002092 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: ends_during ! ends during is_a: starts_during ! starts during @@ -1794,7 +1806,7 @@ name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. xref: RO:0002017 is_a: has_component_process ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -1814,7 +1826,7 @@ xref: RO:0002018 domain: BFO:0000015 range: BFO:0000015 is_a: has_component ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] @@ -1842,8 +1854,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1854,8 +1866,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000000 -range: CARO:0000000 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1875,8 +1887,8 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -1901,12 +1913,12 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_effector_activity name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. xref: RO:0002025 is_functional: true is_a: has_component_activity ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -1969,10 +1981,10 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to -created_by: https://orcid.org/0000-0002-7463-6306 [Typedef] id: has_exposure_receptor @@ -2029,7 +2041,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 -domain: CARO:0001001 +domain: UBERON:0000122 is_a: overlaps ! overlaps [Typedef] @@ -2061,7 +2073,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -2070,8 +2082,8 @@ id: has_high_plasma_membrane_amount name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015015 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2098,6 +2110,7 @@ xref: RO:0002233 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 is_a: has_participant ! has participant inverse_of: input_of ! input of @@ -2135,7 +2148,7 @@ name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] xref: RO:0002019 is_a: has_input ! has input -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] @@ -2143,8 +2156,8 @@ id: has_low_plasma_membrane_amount name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] xref: RO:0015016 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 is_a: has_plasma_membrane_part ! has plasma membrane part @@ -2232,7 +2245,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2244,7 +2257,7 @@ xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2255,7 +2268,7 @@ comment: A has necessary component activity B if A and B are GO molecular functi xref: RO:0002016 is_a: has_component_activity ! has component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [Typedef] @@ -2266,7 +2279,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002014 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: negatively_regulated_by ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -2281,6 +2294,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI is_a: has_participant ! has participant inverse_of: output_of ! output of @@ -2380,8 +2394,8 @@ inverse_of: phenotype_of ! phenotype of id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 -property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string @@ -2397,8 +2411,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 -domain: CARO:0000006 -range: CARO:0000006 +domain: UBERON:0000465 +range: UBERON:0000465 is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -2410,7 +2424,7 @@ comment: By convention GO molecular functions are classified by their effector f xref: RO:0002015 is_a: has_regulatory_component_activity ! has regulatory component activity is_a: positively_regulated_by ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -2481,7 +2495,7 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_00 [Typedef] id: has_primary_input name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input @@ -2502,7 +2516,7 @@ creation_date: 2018-12-13T11:26:17Z [Typedef] id: has_primary_output name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output @@ -2528,7 +2542,7 @@ def: "A 'has regulatory component activity' B if A and B are GO molecular functi xref: RO:0002013 is_a: has_component_activity ! has component activity is_a: regulated_by ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -2543,6 +2557,20 @@ domain: BFO:0000004 range: BFO:0000023 is_a: has_characteristic ! has characteristic +[Typedef] +id: has_roost +name: has roost +def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. +subset: ro-eco +xref: RO:0008509 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 +property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime +property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string +domain: OBI:0100026 +range: ENVO:01000739 +is_a: has_habitat ! has habitat + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2553,7 +2581,7 @@ synonym: "has sensory terminal location" EXACT [] xref: RO:0013007 domain: CL:0000101 is_a: has_dendrite_location ! has dendrite location -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] @@ -2565,8 +2593,8 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: CARO:0000003 -range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +domain: UBERON:0000061 +range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2578,7 +2606,7 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_activator_of ! is small molecule activator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -2588,7 +2616,7 @@ def: "a relation between a process and a continuant, in which the process is inh xref: RO:0012002 is_a: has_small_molecule_regulator ! has small molecule regulator inverse_of: is_small_molecule_inhibitor_of ! is small molecule inhibitor of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] @@ -2598,19 +2626,19 @@ def: "a relation between a process and a continuant, in which the process is reg xref: RO:0012000 is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: has_soma_location name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] xref: RO:0002100 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 -range: CARO:0000003 +range: UBERON:0000465 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2672,7 +2700,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] xref: RO:0013001 is_a: has_synaptic_terminal_in ! has synaptic terminal in -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -2681,7 +2709,7 @@ name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] xref: RO:0013004 is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] @@ -2862,12 +2890,12 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: in_register_with name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] xref: RO:0002026 domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: mereotopologically_related_to ! mereotopologically related to -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] @@ -2896,7 +2924,7 @@ name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] xref: RO:0012011 is_a: causally_upstream_of ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -2907,6 +2935,7 @@ xref: RO:0002409 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: negatively_regulates ! negatively regulates @@ -2936,6 +2965,7 @@ xref: RO:0002407 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI is_transitive: true is_a: indirectly_regulates ! indirectly regulates is_a: positively_regulates ! positively regulates @@ -2966,7 +2996,7 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p xref: RO:0012012 is_a: indirectly_causally_upstream_of ! indirectly causally upstream of is_a: regulates ! regulates -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -3052,7 +3082,7 @@ xref: RO:0002331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of is_a: participates_in ! participates in @@ -3098,12 +3128,13 @@ is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regu [Typedef] id: is_active_in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] xref: RO:0002432 property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI is_a: functionally_related_to ! functionally related to is_a: overlaps ! overlaps @@ -3112,7 +3143,7 @@ id: is_agonist_of name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] xref: RO:0018027 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: directly_positively_regulates_activity_of ! directly positively regulates activity of @@ -3132,7 +3163,7 @@ id: is_antagonist_of name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] xref: RO:0018029 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3311,7 +3342,7 @@ id: is_inverse_agonist_of name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] xref: RO:0018028 -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of @@ -3338,9 +3369,10 @@ id: is_small_molecule_activator_of name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] xref: RO:0012005 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: capable_of_positively_regulating ! capable of positively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -3348,9 +3380,10 @@ id: is_small_molecule_inhibitor_of name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] xref: RO:0012006 +property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: capable_of_negatively_regulating ! capable of negatively regulating is_a: is_small_molecule_regulator_of ! is small molecule regulator of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] @@ -3359,7 +3392,7 @@ name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] xref: RO:0012004 is_a: capable_of_regulating ! capable of regulating -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -3478,7 +3511,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:cjm" xsd:string +property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 is_a: part_of ! part of @@ -3631,7 +3664,7 @@ name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] xref: RO:0002021 is_a: has_part_that_occurs_in ! has part that occurs in -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -3733,6 +3766,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: overlaps ! overlaps inverse_of: has_part ! has part @@ -3801,8 +3835,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 +domain: OBI:0100026 +range: OBI:0100026 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3994,11 +4028,11 @@ id: provides_input_for name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] xref: RO:0002413 -property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: transitively_provides_input_for ! transitively provides input for @@ -4036,7 +4070,7 @@ creation_date: 2017-11-05T03:20:01Z id: realized_in_response_to name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] xref: RO:0009501 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 @@ -4077,7 +4111,7 @@ def: "A relationship between an anatomical structure (including cells) and a neu xref: RO:0013008 is_a: synapsed_by ! synapsed by inverse_of: sends_synaptic_output_to_cell ! sends synaptic output to cell -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] @@ -4087,7 +4121,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013002 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] @@ -4097,7 +4131,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013005 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: receives_synaptic_input_in_region ! receives synaptic input in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] @@ -4214,8 +4248,9 @@ def: "p removes input for q iff p is causally upstream of q, there exists some c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012010 +property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] @@ -4239,7 +4274,7 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string -range: CARO:0000003 +range: UBERON:0000061 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4249,7 +4284,7 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] xref: RO:0012007 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] @@ -4351,7 +4386,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -4414,7 +4449,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -4572,7 +4607,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013006 is_a: has_synaptic_IO_throughout ! has synaptic IO throughout is_a: sends_synaptic_output_to_region ! sends synaptic output to region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] @@ -4582,7 +4617,7 @@ def: "A relationship between a neuron and a cell that it has a functionally rele comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. xref: RO:0013009 is_a: synapsed_to ! synapsed to -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] @@ -4592,7 +4627,7 @@ def: "A relationship between a neuron and a region, where the neuron has a funct xref: RO:0013003 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in is_a: has_synaptic_IO_in_region ! has synaptic IO in region -created_by: http://orcid.org/0000-0002-1373-1705 +created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] @@ -4624,11 +4659,13 @@ range: RO:0002532 [Typedef] id: simultaneous_with name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco xref: RO:0002082 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_symmetric: true is_transitive: true is_a: before_or_simultaneous_with ! before or simultaneous with @@ -4639,8 +4676,8 @@ def: "inverse of has skeleton" [] subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: part_of ! part of [Typedef] @@ -5007,7 +5044,7 @@ name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] xref: RO:0002020 is_a: transports_or_maintains_localization_of ! transports or maintains localization of -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 286fb05e..d131f24e 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -147,24 +147,6 @@ - - - - - - - - - - - - - - - - - - @@ -189,6 +171,12 @@ + + + + + + @@ -301,6 +289,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -820,7 +809,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity @@ -835,7 +824,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity @@ -851,7 +840,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity @@ -866,7 +855,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity @@ -880,7 +869,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-05-24T09:44:33Z RO:0002017 has_component_activity @@ -897,7 +886,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z RO:0002018 has_component_process @@ -911,7 +900,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + 2017-07-19T17:30:36Z RO:0002019 has_ligand @@ -925,7 +914,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + 2017-07-20T17:11:08Z RO:0002020 transports @@ -939,7 +928,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + 2017-07-20T17:19:37Z RO:0002021 occurs_across @@ -953,7 +942,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - dos + 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by @@ -964,7 +953,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -975,7 +964,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by @@ -985,7 +974,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -996,7 +985,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by @@ -1006,7 +995,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1017,7 +1006,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z RO:0002025 has_effector_activity @@ -1028,7 +1017,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -1047,7 +1036,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + 2017-12-07T12:58:06Z RO:0002026 in_register_with @@ -1064,7 +1053,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + @@ -1088,7 +1077,9 @@ Examples include: the relationship between two channels collected simultaneously + + x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 @@ -1257,6 +1248,7 @@ Examples include: the relationship between two channels collected simultaneously happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1282,9 +1274,9 @@ Examples include: the relationship between two channels collected simultaneously - + - Relation between a neuron and an anatomical structure that its soma is part of. + Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) @@ -1302,7 +1294,7 @@ Examples include: the relationship between two channels collected simultaneously - + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. @@ -1393,8 +1385,8 @@ Examples include: the relationship between two channels collected simultaneously - - + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1706,7 +1698,7 @@ N1 SubclassOf ( - + @@ -1877,8 +1869,8 @@ N1 SubclassOf ( - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 @@ -1943,8 +1935,8 @@ N1 SubclassOf ( - + @@ -2026,16 +2018,16 @@ N1 SubclassOf ( - + - + @@ -2342,7 +2334,7 @@ N1 SubclassOf ( - + x develops_in y if x is located in y whilst x is developing @@ -2469,6 +2461,7 @@ N1 SubclassOf ( has_input has input + https://wiki.geneontology.org/Has_input @@ -2489,6 +2482,7 @@ N1 SubclassOf ( has_output has output + https://wiki.geneontology.org/Has_output @@ -2678,8 +2672,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2712,8 +2706,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - - + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T @@ -2828,7 +2822,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho acts_upstream_of_or_within acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2882,7 +2876,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. @@ -3027,7 +3021,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3059,6 +3053,7 @@ where causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3076,6 +3071,7 @@ where causally_upstream_of,_negative_effect causally upstream of, negative effect + @@ -3138,7 +3134,7 @@ where - + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity @@ -3254,6 +3250,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati contributes_to contributes to + https://wiki.geneontology.org/Contributes_to @@ -3276,6 +3273,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables + https://wiki.geneontology.org/Enables @@ -3319,7 +3317,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002331 involved_in involved in - + https://wiki.geneontology.org/Involved_in @@ -3353,6 +3351,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enabled_by enabled by + https://wiki.geneontology.org/Enabled_by @@ -3724,7 +3723,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) @@ -3736,7 +3735,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle to create a stricter domain constraint @@ -3747,7 +3746,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) @@ -3759,7 +3758,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + We need to import uberon muscle into RO to use as a stricter domain constraint @@ -3948,8 +3947,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). @@ -4077,6 +4076,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002407 indirectly_positively_regulates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4094,6 +4094,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002409 indirectly_negatively_regulates indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4170,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit directly provides input for @@ -4178,6 +4178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different RO:0002413 provides_input_for provides input for + https://wiki.geneontology.org/Provides_input_for @@ -4308,13 +4309,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different is_active_in is active in + https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -5485,8 +5487,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. @@ -5499,7 +5501,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. @@ -5654,8 +5656,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -5722,7 +5724,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - GOC:cjm + RO:0002571 lumen_of @@ -5750,8 +5752,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + RO:0002574 @@ -5766,8 +5768,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + inverse of has skeleton RO:0002576 @@ -6146,6 +6148,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_positively_regulates directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -6165,6 +6168,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly_negatively_regulates directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -6612,7 +6616,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6638,7 +6642,7 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm + GOC:dph GOC:kva GOC:pt @@ -6801,7 +6805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) @@ -6891,7 +6895,7 @@ Environmental exposures include those imposed by natural environments, experimen - + disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z @@ -6911,8 +6915,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6937,8 +6941,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + @@ -6995,7 +6999,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z @@ -7031,7 +7035,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -7047,6 +7051,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -7064,7 +7069,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_positive_effect acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -7082,7 +7087,7 @@ Environmental exposures include those imposed by natural environments, experimen acts_upstream_of,_negative_effect acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -7097,6 +7102,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -7111,6 +7117,7 @@ Environmental exposures include those imposed by natural environments, experimen RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect + @@ -7173,8 +7180,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -7188,8 +7195,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with @@ -7223,6 +7230,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) + x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. + + 2023-01-18T14:28:21Z + RO:0008509 + + has_roost + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. + has roost + + + + @@ -7247,7 +7273,7 @@ Environmental exposures include those imposed by natural environments, experimen triggered by process - RO:cjm + @@ -7481,7 +7507,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator @@ -7496,7 +7522,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator @@ -7511,7 +7537,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor @@ -7525,7 +7551,7 @@ For example, protein A (transcription factor) indirectly increases by expression p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + 2020-06-08T17:21:33Z RO:0012003 @@ -7542,7 +7568,7 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of @@ -7557,11 +7583,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of + https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -7572,11 +7599,12 @@ For example, protein A (transcription factor) indirectly increases by expression a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of + https://wiki.geneontology.org/Is_small_molecule_inhibitor_of @@ -7586,7 +7614,7 @@ For example, protein A (transcription factor) indirectly increases by expression The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of @@ -7599,7 +7627,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + 2021-02-26T07:28:29Z RO:0012008 @@ -7616,13 +7644,14 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of + https://wiki.geneontology.org/Constitutively_upstream_of @@ -7632,13 +7661,14 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for + https://wiki.geneontology.org/Removes_input_for @@ -7648,7 +7678,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of @@ -7663,7 +7693,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates @@ -7677,7 +7707,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - + 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in @@ -7693,7 +7723,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - + 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region @@ -7708,7 +7738,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - + 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region @@ -7722,7 +7752,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout @@ -7737,7 +7767,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout @@ -7752,7 +7782,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - + 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout @@ -7767,7 +7797,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - + 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location @@ -7785,7 +7815,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - + 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron @@ -7799,7 +7829,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - + 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell @@ -7814,7 +7844,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - + RO:0014001 disease_has_infectious_agent disease has infectious agent @@ -7845,8 +7875,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - + + RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount @@ -7867,8 +7897,8 @@ For example, protein A (transcription factor) indirectly increases by expression 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - + + RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount @@ -7886,8 +7916,8 @@ For example, protein A (transcription factor) indirectly increases by expression Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z + + 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease @@ -7901,8 +7931,8 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z + + 2021-11-05T17:30:44Z RO:0016002 has_disease has disease @@ -7917,8 +7947,8 @@ For example, protein A (transcription factor) indirectly increases by expression X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 - 2021-12-14T20:41:45Z - + + 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium @@ -7959,7 +7989,7 @@ For example, protein A (transcription factor) indirectly increases by expression mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - + RO:0018027 is_agonist_of is agonist of @@ -7974,7 +8004,7 @@ For example, protein A (transcription factor) indirectly increases by expression pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - + RO:0018028 is_inverse_agonist_of is inverse agonist of @@ -7989,7 +8019,7 @@ For example, protein A (transcription factor) indirectly increases by expression tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - + RO:0018029 is_antagonist_of is antagonist of @@ -8044,7 +8074,7 @@ For example, protein A (transcription factor) indirectly increases by expression Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - + RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition @@ -8169,48 +8199,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -8235,6 +8223,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8247,6 +8241,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8295,6 +8295,42 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-time-interval.tsv b/subsets/ro-time-interval.tsv index 8eb702f1..406af670 100644 --- a/subsets/ro-time-interval.tsv +++ b/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid1 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid18 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid22 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid26 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid33 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid37 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid40 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid5 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid52 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid58 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid61 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid64 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid67 -_:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid9 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid1 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid18 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid22 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid26 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid33 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid37 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid40 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid5 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid52 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid58 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid61 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid64 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid67 +_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid9 @@ -26,19 +26,14 @@ _:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid9 - - - - - - - + + @@ -47,5 +42,11 @@ _:B61851834X2D5e9aX2D4c66X2D8005X2D8b5e3ee70d15genid9 + + + + + +