diff --git a/releases/current/debio.json b/releases/current/debio.json
index ddcf2c8..7448ba0 100644
--- a/releases/current/debio.json
+++ b/releases/current/debio.json
@@ -13,7 +13,7 @@
"val" : "bio2obo:debio"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#date",
- "val" : "13:12:2023 15:32"
+ "val" : "04:01:2024 15:37"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
"val" : "1.2"
@@ -25,104 +25,140 @@
"lbl" : "definition",
"type" : "PROPERTY"
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000001",
- "lbl" : "gene product is a member of",
+ "id" : "http://purl.obolibrary.org/obo/RO_0000015",
+ "lbl" : "has functional parent",
"type" : "PROPERTY",
"meta" : {
+ "definition" : {
+ "val" : "X has functional parent Y if X is a derivative (e.g., a salt) of Y. E.g., bepridil hydrochloride has functional parent bepridil"
+ },
+ "xrefs" : [ {
+ "val" : "RO:0000015"
+ }, {
+ "val" : "obo:chebi#has_functional_parent"
+ } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000002",
- "lbl" : "has mature miRNA",
+ "id" : "http://purl.obolibrary.org/obo/RO_0018033",
+ "lbl" : "is conjugate base of",
"type" : "PROPERTY",
"meta" : {
+ "definition" : {
+ "val" : "X is conjugate base of Y typically means that X is a deprotonated form of Y"
+ },
+ "xrefs" : [ {
+ "val" : "RO:0018033"
+ }, {
+ "val" : "obo:chebi#is_conjugate_base_of"
+ } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000003",
- "lbl" : "species specific",
+ "id" : "http://purl.obolibrary.org/obo/RO_0018034",
+ "lbl" : "is conjugate acid of",
"type" : "PROPERTY",
"meta" : {
"definition" : {
- "val" : "X speciesSpecific Y means that Y is a general phenomena, like a pathway, and X is the version that appears in a species. X should state which species with RO:0002162 (in taxon)"
+ "val" : "X is conjugate acid of Y typically means that Y is a protonated form of X"
},
+ "xrefs" : [ {
+ "val" : "RO:0018034"
+ }, {
+ "val" : "obo:chebi#is_conjugate_acid_of"
+ } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000004",
- "lbl" : "Antibody has target",
+ "id" : "http://purl.obolibrary.org/obo/RO_0018036",
+ "lbl" : "is tautomer of",
"type" : "PROPERTY",
"meta" : {
+ "definition" : {
+ "val" : "X and Y are tautomers if they are different realizations of the resonance structure of the same molecule"
+ },
+ "xrefs" : [ {
+ "val" : "RO:0018036"
+ }, {
+ "val" : "obo:chebi#is_tautomer_of"
+ } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000005",
- "lbl" : "locus group",
+ "id" : "http://purl.obolibrary.org/obo/RO_0018039",
+ "lbl" : "is enantiomer of",
"type" : "PROPERTY",
"meta" : {
+ "definition" : {
+ "val" : "X and Y are in an enantiomeric relationship if flipping all stereocenters of X results in Y"
+ },
+ "xrefs" : [ {
+ "val" : "RO:0018039"
+ }, {
+ "val" : "obo:chebi#is_enantiomer_of"
+ } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
- }, {
- "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag",
- "val" : "true"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000006",
- "lbl" : "has salt",
+ "id" : "http://purl.obolibrary.org/obo/RO_0018040",
+ "lbl" : "has parent hydride",
"type" : "PROPERTY",
"meta" : {
+ "definition" : {
+ "val" : "X has parent hydride Y if the substituents on X are replaced with hydrogens. E.g., SbCl3 has parent hydride SbH3"
+ },
+ "xrefs" : [ {
+ "val" : "RO:0018040"
+ }, {
+ "val" : "obo:chebi#has_parent_hydride"
+ } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000007",
- "lbl" : "has left-to-right reaction",
+ "id" : "http://purl.obolibrary.org/obo/debio_0000001",
+ "lbl" : "gene product is a member of",
"type" : "PROPERTY",
"meta" : {
- "definition" : {
- "val" : "X ltr Y means reaction X of undetermined direction has a left-to-right reaction Y. Relevant for Rhea."
- },
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000008",
- "lbl" : "has right-to-left reaction",
+ "id" : "http://purl.obolibrary.org/obo/debio_0000002",
+ "lbl" : "has mature miRNA",
"type" : "PROPERTY",
"meta" : {
- "definition" : {
- "val" : "X rtl Y means reaction X of undetermined direction has a right-to-left reaction Y. Relevant for Rhea."
- },
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000009",
- "lbl" : "has bi-directional reaction",
+ "id" : "http://purl.obolibrary.org/obo/debio_0000003",
+ "lbl" : "species specific",
"type" : "PROPERTY",
"meta" : {
"definition" : {
- "val" : "X bi Y means reaction X of undetermined direction has a bidirectional reaction Y. Relevant for Rhea."
+ "val" : "X speciesSpecific Y means that Y is a general phenomena, like a pathway, and X is the version that appears in a species. X should state which species with RO:0002162 (in taxon)"
},
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
@@ -130,96 +166,72 @@
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000010",
- "lbl" : "is conjugate base of",
+ "id" : "http://purl.obolibrary.org/obo/debio_0000004",
+ "lbl" : "Antibody has target",
"type" : "PROPERTY",
"meta" : {
- "definition" : {
- "val" : "X is conjugate base of Y typically means that X is a deprotonated form of Y"
- },
- "xrefs" : [ {
- "val" : "obo:chebi#is_conjugate_base_of"
- } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000011",
- "lbl" : "is conjugate acid of",
+ "id" : "http://purl.obolibrary.org/obo/debio_0000005",
+ "lbl" : "locus group",
"type" : "PROPERTY",
"meta" : {
- "definition" : {
- "val" : "X is conjugate acid of Y typically means that Y is a protonated form of X"
- },
- "xrefs" : [ {
- "val" : "obo:chebi#is_conjugate_acid_of"
- } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
+ }, {
+ "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag",
+ "val" : "true"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000012",
- "lbl" : "is enantiomer of",
+ "id" : "http://purl.obolibrary.org/obo/debio_0000006",
+ "lbl" : "has salt",
"type" : "PROPERTY",
"meta" : {
- "definition" : {
- "val" : "X and Y are in an enantiomeric relationship if flipping all stereocenters of X results in Y"
- },
- "xrefs" : [ {
- "val" : "obo:chebi#is_enantiomer_of"
- } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000013",
- "lbl" : "is tautomer of",
+ "id" : "http://purl.obolibrary.org/obo/debio_0000007",
+ "lbl" : "has left-to-right reaction",
"type" : "PROPERTY",
"meta" : {
"definition" : {
- "val" : "X and Y are tautomers if they are different realizations of the resonance structure of the same molecule"
+ "val" : "X ltr Y means reaction X of undetermined direction has a left-to-right reaction Y. Relevant for Rhea."
},
- "xrefs" : [ {
- "val" : "obo:chebi#is_tautomer_of"
- } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000014",
- "lbl" : "has parent hydride",
+ "id" : "http://purl.obolibrary.org/obo/debio_0000008",
+ "lbl" : "has right-to-left reaction",
"type" : "PROPERTY",
"meta" : {
"definition" : {
- "val" : "X has parent hydride Y if the substituents on X are replaced with hydrogens. E.g., SbCl3 has parent hydride SbH3"
+ "val" : "X rtl Y means reaction X of undetermined direction has a right-to-left reaction Y. Relevant for Rhea."
},
- "xrefs" : [ {
- "val" : "obo:chebi#has_parent_hydride"
- } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
} ]
}
}, {
- "id" : "http://purl.obolibrary.org/obo/debio_0000015",
- "lbl" : "has functional parent",
+ "id" : "http://purl.obolibrary.org/obo/debio_0000009",
+ "lbl" : "has bi-directional reaction",
"type" : "PROPERTY",
"meta" : {
"definition" : {
- "val" : "X has functional parent Y if X is a derivative (e.g., a salt) of Y. E.g., bepridil hydrochloride has functional parent bepridil"
+ "val" : "X bi Y means reaction X of undetermined direction has a bidirectional reaction Y. Relevant for Rhea."
},
- "xrefs" : [ {
- "val" : "obo:chebi#has_functional_parent"
- } ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "orcid:0000-0003-4423-4370"
diff --git a/releases/current/debio.obo b/releases/current/debio.obo
index 8d59238..cfeac8e 100644
--- a/releases/current/debio.obo
+++ b/releases/current/debio.obo
@@ -1,5 +1,5 @@
format-version: 1.2
-date: 13:12:2023 15:32
+date: 04:01:2024 15:37
auto-generated-by: bio2obo:debio
data-version: 0.1.2-dev
idspace: RO http://purl.obolibrary.org/obo/RO_
@@ -67,6 +67,7 @@ name: is conjugate base of
def: "X is conjugate base of Y typically means that X is a deprotonated form of Y"
created_by: orcid:0000-0003-4423-4370
xref: obo:chebi#is_conjugate_base_of
+xref: RO:0018033
[Typedef]
id: debio:0000011
@@ -74,6 +75,7 @@ name: is conjugate acid of
def: "X is conjugate acid of Y typically means that Y is a protonated form of X"
created_by: orcid:0000-0003-4423-4370
xref: obo:chebi#is_conjugate_acid_of
+xref: RO:0018034
[Typedef]
id: debio:0000012
@@ -81,6 +83,7 @@ name: is enantiomer of
def: "X and Y are in an enantiomeric relationship if flipping all stereocenters of X results in Y"
created_by: orcid:0000-0003-4423-4370
xref: obo:chebi#is_enantiomer_of
+xref: RO:0018039
[Typedef]
id: debio:0000013
@@ -88,6 +91,7 @@ name: is tautomer of
def: "X and Y are tautomers if they are different realizations of the resonance structure of the same molecule"
created_by: orcid:0000-0003-4423-4370
xref: obo:chebi#is_tautomer_of
+xref: RO:0018036
[Typedef]
id: debio:0000014
@@ -95,6 +99,7 @@ name: has parent hydride
def: "X has parent hydride Y if the substituents on X are replaced with hydrogens. E.g., SbCl3 has parent hydride SbH3"
created_by: orcid:0000-0003-4423-4370
xref: obo:chebi#has_parent_hydride
+xref: RO:0018040
[Typedef]
id: debio:0000015
@@ -102,6 +107,7 @@ name: has functional parent
def: "X has functional parent Y if X is a derivative (e.g., a salt) of Y. E.g., bepridil hydrochloride has functional parent bepridil"
created_by: orcid:0000-0003-4423-4370
xref: obo:chebi#has_functional_parent
+xref: RO:0000015
[Typedef]
id: debio:0000016
diff --git a/releases/current/debio.owl b/releases/current/debio.owl
index 88b37ed..ffe533a 100644
--- a/releases/current/debio.owl
+++ b/releases/current/debio.owl
@@ -14,7 +14,7 @@
A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON.Decentralized Biomedical Ontologybio2obo:debio
- 13:12:2023 15:32
+ 04:01:2024 15:371.2
@@ -313,6 +313,19 @@
+
+
+
+ X has functional parent Y if X is a derivative (e.g., a salt) of Y. E.g., bepridil hydrochloride has functional parent bepridil
+ orcid:0000-0003-4423-4370
+ RO:0000015
+ obo:chebi#has_functional_parent
+ debio:0000015
+ has functional parent
+
+
+
+
@@ -325,6 +338,71 @@
+
+
+
+ X is conjugate base of Y typically means that X is a deprotonated form of Y
+ orcid:0000-0003-4423-4370
+ RO:0018033
+ obo:chebi#is_conjugate_base_of
+ debio:0000010
+ is conjugate base of
+
+
+
+
+
+
+
+ X is conjugate acid of Y typically means that Y is a protonated form of X
+ orcid:0000-0003-4423-4370
+ RO:0018034
+ obo:chebi#is_conjugate_acid_of
+ debio:0000011
+ is conjugate acid of
+
+
+
+
+
+
+
+ X and Y are tautomers if they are different realizations of the resonance structure of the same molecule
+ orcid:0000-0003-4423-4370
+ RO:0018036
+ obo:chebi#is_tautomer_of
+ debio:0000013
+ is tautomer of
+
+
+
+
+
+
+
+ X and Y are in an enantiomeric relationship if flipping all stereocenters of X results in Y
+ orcid:0000-0003-4423-4370
+ RO:0018039
+ obo:chebi#is_enantiomer_of
+ debio:0000012
+ is enantiomer of
+
+
+
+
+
+
+
+ X has parent hydride Y if the substituents on X are replaced with hydrogens. E.g., SbCl3 has parent hydride SbH3
+ orcid:0000-0003-4423-4370
+ RO:0018040
+ obo:chebi#has_parent_hydride
+ debio:0000014
+ has parent hydride
+
+
+
+
@@ -413,78 +491,6 @@
-
-
-
- X is conjugate base of Y typically means that X is a deprotonated form of Y
- orcid:0000-0003-4423-4370
- obo:chebi#is_conjugate_base_of
- debio:0000010
- is conjugate base of
-
-
-
-
-
-
-
- X is conjugate acid of Y typically means that Y is a protonated form of X
- orcid:0000-0003-4423-4370
- obo:chebi#is_conjugate_acid_of
- debio:0000011
- is conjugate acid of
-
-
-
-
-
-
-
- X and Y are in an enantiomeric relationship if flipping all stereocenters of X results in Y
- orcid:0000-0003-4423-4370
- obo:chebi#is_enantiomer_of
- debio:0000012
- is enantiomer of
-
-
-
-
-
-
-
- X and Y are tautomers if they are different realizations of the resonance structure of the same molecule
- orcid:0000-0003-4423-4370
- obo:chebi#is_tautomer_of
- debio:0000013
- is tautomer of
-
-
-
-
-
-
-
- X has parent hydride Y if the substituents on X are replaced with hydrogens. E.g., SbCl3 has parent hydride SbH3
- orcid:0000-0003-4423-4370
- obo:chebi#has_parent_hydride
- debio:0000014
- has parent hydride
-
-
-
-
-
-
-
- X has functional parent Y if X is a derivative (e.g., a salt) of Y. E.g., bepridil hydrochloride has functional parent bepridil
- orcid:0000-0003-4423-4370
- obo:chebi#has_functional_parent
- debio:0000015
- has functional parent
-
-
-
-
diff --git a/src/debio/resources/typedefs.json b/src/debio/resources/typedefs.json
index 1c00a51..6c19f66 100644
--- a/src/debio/resources/typedefs.json
+++ b/src/debio/resources/typedefs.json
@@ -73,6 +73,10 @@
{
"prefix": "obo",
"identifier": "chebi#is_conjugate_base_of"
+ },
+ {
+ "prefix": "ro",
+ "identifier": "0018033"
}
]
},
@@ -86,6 +90,10 @@
{
"prefix": "obo",
"identifier": "chebi#is_conjugate_acid_of"
+ },
+ {
+ "prefix": "ro",
+ "identifier": "0018034"
}
]
},
@@ -99,6 +107,9 @@
{
"prefix": "obo",
"identifier": "chebi#is_enantiomer_of"
+ },{
+ "prefix": "ro",
+ "identifier": "0018039"
}
]
},
@@ -112,6 +123,9 @@
{
"prefix": "obo",
"identifier": "chebi#is_tautomer_of"
+ },{
+ "prefix": "ro",
+ "identifier": "0018036"
}
]
},
@@ -125,6 +139,9 @@
{
"prefix": "obo",
"identifier": "chebi#has_parent_hydride"
+ },{
+ "prefix": "ro",
+ "identifier": "0018040"
}
]
},
@@ -138,6 +155,9 @@
{
"prefix": "obo",
"identifier": "chebi#has_functional_parent"
+ },{
+ "prefix": "ro",
+ "identifier": "0000015"
}
]
},