rename "exposure event or process" to "exposure of organism" (issue 5…

…99) (#606) * add exposure event class * change domain of 'related via exposure to' to 'exposure event' * obsolete 'exposure event or process' * add exposure of organism to cob_terms * remove creator "cmartin" (I do not know the ORICID) * change label to exposure of organism * chhange IRI to COB_0001000 * update 'id' annotation to COB:0001000 and removed editor note I thought was confusing * undo `cl_import` change * import `COB:0001000` properly --------- Co-authored-by: Anita Caron <[email protected]> Co-authored-by: Anita Caron <[email protected]>
oborel · Feb 9, 2024 · 3428cae · 3428cae
1 parent 9e03509
commit 3428cae
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Showing 3 changed files with 20 additions and 9 deletions.
diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/ro/imports/cob_import.owl>
-<http://purl.obolibrary.org/obo/ro/releases/2023-08-23/imports/cob_import.owl>
-Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cob/releases/2023-05-12/cob.owl>)
-Annotation(owl:versionInfo "2023-08-23"^^xsd:string)
+<http://purl.obolibrary.org/obo/ro/releases/2024-02-09/imports/cob_import.owl>
+Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cob/releases/2023-11-16/cob.owl>)
+Annotation(owl:versionInfo "2024-02-09")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
@@ -21,6 +21,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000141>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000121>))
+Declaration(Class(<http://purl.obolibrary.org/obo/COB_0001000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0003674>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005634>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0008150>))
@@ -38,7 +39,9 @@ Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002333>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000117>))
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/description>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
+Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/title>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
 Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#exactMatch>))
 ############################
@@ -167,6 +170,12 @@ SubClassOf(<http://purl.obolibrary.org/obo/CL_0000000> <http://purl.obolibrary.o
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/COB_0000121> "measurement datum")
 
+# Class: <http://purl.obolibrary.org/obo/COB_0001000> (exposure of organism)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/COB_0001000> "A process during which an organism comes into contact with another entity.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/COB_0001000> "exposure of organism"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/COB_0001000> <http://purl.obolibrary.org/obo/BFO_0000015>)
+
 # Class: <http://purl.obolibrary.org/obo/GO_0003674> (gene product or complex activity)
 
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0003674> "This is the same as GO molecular function")
@@ -188,4 +197,4 @@ SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.o
 SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/GO_0003674>))
 
 
-)
+)
diff --git a/src/ontology/imports/cob_terms.txt b/src/ontology/imports/cob_terms.txt
@@ -1 +1,2 @@
 COB:0000121
+COB:0001000
diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl
@@ -42,6 +42,7 @@ Annotation(foaf:homepage " https://github.com/oborel/obo-relations/"^^xsd:anyURI
 Declaration(Class(obo:BFO_0000019))
 Declaration(Class(obo:BFO_0000031))
 Declaration(Class(obo:CHEBI_50906))
+Declaration(Class(obo:COB_0001000))
 Declaration(Class(obo:OGMS_0000031))
 Declaration(Class(obo:RO_0002310))
 Declaration(Class(obo:RO_0002532))
@@ -2672,7 +2673,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002244 "Any relationship between an
 AnnotationAssertion(obo:IAO_0000232 obo:RO_0002244 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.")
 AnnotationAssertion(rdfs:label obo:RO_0002244 "related via exposure to")
 SubObjectPropertyOf(obo:RO_0002244 obo:RO_0002410)
-ObjectPropertyDomain(obo:RO_0002244 obo:RO_0002310)
+ObjectPropertyDomain(obo:RO_0002244 obo:COB_0001000)
 
 # Object Property: obo:RO_0002245 (over-expressed in)
 
@@ -6904,18 +6905,18 @@ SubClassOf(obo:GO_0016301 ObjectHasSelf(obo:RO_0002481))
 
 SubClassOf(obo:GO_0019107 ObjectHasSelf(obo:RO_0018001))
 
-# Class: obo:RO_0002310 (exposure event or process)
+# Class: obo:RO_0002310 (obsolete exposure event or process)
 
 AnnotationAssertion(obo:IAO_0000112 obo:RO_0002310 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,")
 AnnotationAssertion(obo:IAO_0000112 obo:RO_0002310 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes."^^xsd:anyURI)
-AnnotationAssertion(obo:IAO_0000115 obo:RO_0002310 "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.")
+AnnotationAssertion(obo:IAO_0000115 obo:RO_0002310 "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.")
 AnnotationAssertion(obo:IAO_0000116 obo:RO_0002310 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.")
 AnnotationAssertion(terms:creator obo:RO_0002310 <https://orcid.org/0000-0002-6601-2165>)
 AnnotationAssertion(oboInOwl:created_by obo:RO_0002310 <https://orcid.org/0000-0002-6601-2165>)
 AnnotationAssertion(oboInOwl:creation_date obo:RO_0002310 "2017-06-05T17:55:39Z"^^xsd:dateTime)
-AnnotationAssertion(rdfs:label obo:RO_0002310 "exposure event or process")
+AnnotationAssertion(rdfs:label obo:RO_0002310 "obsolete exposure event or process")
 AnnotationAssertion(rdfs:seeAlso obo:RO_0002310 "https://github.com/oborel/obo-relations/pull/173"^^xsd:anyURI)
-SubClassOf(obo:RO_0002310 obo:BFO_0000015)
+AnnotationAssertion(owl:deprecated obo:RO_0002310 "true"^^xsd:boolean)
 
 # Class: obo:RO_0002532 (sequentially ordered entity)