Merge branch 'master' into issue-#598-part2

core.json

@@ -7,12 +7,12 @@
         "val" : "https://creativecommons.org/publicdomain/zero/1.0/"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2024-02-13"
+        "val" : "2024-04-24"
       }, {
         "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/2024-02-13/core.json"
+      "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-04-24/core.json"
     },
     "nodes" : [ {
       "id" : "http://purl.obolibrary.org/obo/BFO_0000002",

core.obo

@@ -1,9 +1,9 @@
 format-version: 1.2
-data-version: ro/releases/2024-02-13/core.owl
+data-version: ro/releases/2024-04-24/core.owl
 ontology: ro/core
 property_value: http://purl.org/dc/terms/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 "2024-02-13" xsd:string
+property_value: owl:versionInfo "2024-04-24" xsd:string
 
 [Term]
 id: BFO:0000002

core.owl

@@ -13,9 +13,9 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro/core.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2024-02-13/core.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2024-04-24/core.owl"/>
         <terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
-        <owl:versionInfo>2024-02-13</owl:versionInfo>
+        <owl:versionInfo>2024-04-24</owl:versionInfo>
         <foaf:homepage rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/oborel/obo-relations/wiki/ROCore</foaf:homepage>
     </owl:Ontology>
 

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/2024-03-02/imports/cob_import.owl>
+<http://purl.obolibrary.org/obo/ro/releases/2024-04-05/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 "2024-03-02")
+Annotation(owl:versionInfo "2024-04-05")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
@@ -25,6 +25,7 @@ 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>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000070>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000054>))
@@ -57,45 +58,14 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000115> "def
 #   Object Properties
 ############################
 
-# Object Property: <http://purl.obolibrary.org/obo/BFO_0000050> (<http://purl.obolibrary.org/obo/BFO_0000050>)
-
-InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000051>)
-TransitiveObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>)
-
 # Object Property: <http://purl.obolibrary.org/obo/BFO_0000054> (realized in)
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000054> "realized in"@en)
 
-# Object Property: <http://purl.obolibrary.org/obo/BFO_0000066> (<http://purl.obolibrary.org/obo/BFO_0000066>)
-
-InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000067>)
-ObjectPropertyDomain(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000015>)
-
 # Object Property: <http://purl.obolibrary.org/obo/BFO_0000067> (contains process)
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000067> "contains process"@en)
 
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000052> (<http://purl.obolibrary.org/obo/RO_0000052>)
-
-InverseObjectProperties(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/RO_0000053>)
-
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000053> (<http://purl.obolibrary.org/obo/RO_0000053>)
-
-InverseFunctionalObjectProperty(<http://purl.obolibrary.org/obo/RO_0000053>)
-ObjectPropertyRange(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/BFO_0000020>)
-
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000056> (<http://purl.obolibrary.org/obo/RO_0000056>)
-
-InverseObjectProperties(<http://purl.obolibrary.org/obo/RO_0000056> <http://purl.obolibrary.org/obo/RO_0000057>)
-
-# Object Property: <http://purl.obolibrary.org/obo/RO_0000057> (<http://purl.obolibrary.org/obo/RO_0000057>)
-
-ObjectPropertyDomain(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/BFO_0000015>)
-
-# Object Property: <http://purl.obolibrary.org/obo/RO_0002333> (<http://purl.obolibrary.org/obo/RO_0002333>)
-
-SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0002333> <http://purl.obolibrary.org/obo/RO_0000057>)
-
 
 
 ############################
@@ -105,7 +75,6 @@ SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0002333> <http://purl.obo
 # Class: <http://purl.obolibrary.org/obo/BFO_0000015> (process)
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000015> "process"@en)
-SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000015> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000015>))
 
 # Class: <http://purl.obolibrary.org/obo/BFO_0000016> (disposition)
 
@@ -122,7 +91,6 @@ SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000017> <http://purl.obolibrary.
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000020> "characteristic"@en)
 AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/BFO_0000020> "https://github.com/OBOFoundry/COB/issues/65")
 AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/BFO_0000020> "https://github.com/oborel/obo-relations/pull/284")
-SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000020> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/BFO_0000020>))
 
 # Class: <http://purl.obolibrary.org/obo/BFO_0000023> (role)
 
@@ -178,7 +146,11 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0008150> "A biological process is an evolved process")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0008150> "biological process"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.org/obo/BFO_0000015>)
-SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/GO_0003674>))
+
+# Class: <http://purl.obolibrary.org/obo/OBI_0000070> (assay)
+
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0000070> "assay"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000070> <http://purl.obolibrary.org/obo/BFO_0000015>)
 
 
 )

src/ontology/imports/cob_terms.txt

@@ -1,2 +1,3 @@
+BFO:0000020
 COB:0000121
 COB:0001000

src/ontology/imports/obi_import.owl

@@ -13,6 +13,10 @@ Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/
 Annotation(owl:versionInfo "2023-08-16")
 
 
+Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
+Declaration(Class(<http://purl.obolibrary.org/obo/GO_0008150>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000011>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000070>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000047>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000967>))
@@ -33,6 +37,39 @@ Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
 #   Classes
 ############################
 
+# Class: <http://purl.obolibrary.org/obo/GO_0008150> (<http://purl.obolibrary.org/obo/GO_0008150>)
+
+DisjointClasses(<http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.org/obo/OBI_0000011>)
+
+# Class: <http://purl.obolibrary.org/obo/OBI_0000011> (planned process)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0000011> "planned process"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0000011> "planned process")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/OBI_0000011> "Injecting mice with a vaccine in order to test its efficacy")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/OBI_0000011> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000011> "A process that realizes a plan which is the concretization of a plan specification."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/OBI_0000011> "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/OBI_0000011> "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some 
+objectives is a planned process.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OBI_0000011> "Bjoern Peters")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/OBI_0000011> "branch derived")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0000011> "planned process"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000011> <http://purl.obolibrary.org/obo/BFO_0000015>)
+
+# Class: <http://purl.obolibrary.org/obo/OBI_0000070> (assay)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0000070> "assay"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/OBI_0000070> "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/OBI_0000070> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000070> "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/OBI_0000070> "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OBI_0000070> "PlanAndPlannedProcess Branch"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/OBI_0000070> "measuring"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/OBI_0000070> "scientific observation"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/OBI_0000070> "OBI branch derived"@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0000070> "assay"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000070> <http://purl.obolibrary.org/obo/OBI_0000011>)
+
 # Class: <http://purl.obolibrary.org/obo/OBI_0000047> (processed material)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0000047> "processed material"@en)
@@ -96,4 +133,5 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0100026> "org
 SubClassOf(<http://purl.obolibrary.org/obo/OBI_0100026> <http://purl.obolibrary.org/obo/BFO_0000040>)
 
 
+
 )

src/ontology/imports/obi_terms.txt

@@ -1,4 +1,7 @@
+OBI:0000011
+OBI:0000070
 OBI:0100026
 OBI:0000047
 OBI:0000967
 OBI:0000968
+

src/ontology/imports/orcidio_import.owl

@@ -7,12 +7,13 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/ro/imports/orcidio_import.owl>
-<http://purl.obolibrary.org/obo/ro/releases/2024-02-12/imports/orcidio_import.owl>
-Annotation(owl:versionInfo "2024-02-12")
+<http://purl.obolibrary.org/obo/ro/releases/2024-04-04/imports/orcidio_import.owl>
+Annotation(owl:versionInfo "2024-04-04")
 
 Declaration(NamedIndividual(<https://orcid.org/0000-0001-6677-8489>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0001-6996-0040>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0001-7258-9596>))
+Declaration(NamedIndividual(<https://orcid.org/0000-0001-8314-2140>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0001-8910-9851>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0001-9625-1899>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0002-2908-3327>))
@@ -30,6 +31,7 @@ Declaration(NamedIndividual(<https://orcid.org/0000-0003-1813-6857>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0003-1834-3856>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0003-1909-9269>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0003-1940-6740>))
+Declaration(NamedIndividual(<https://orcid.org/0000-0003-2620-0345>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0003-3138-4118>))
 Declaration(NamedIndividual(<https://orcid.org/0000-0003-4423-4370>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/creator>))
@@ -58,6 +60,11 @@ AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wik
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q57023310>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0001-7258-9596> "researcher")
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q57023310>) rdfs:label <https://orcid.org/0000-0001-7258-9596> "Shawn Zheng Kai Tan")
 
+# Individual: <https://orcid.org/0000-0001-8314-2140> (Raymund Stefancsik)
+
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q52097457>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0001-8314-2140> "researcher")
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q52097457>) rdfs:label <https://orcid.org/0000-0001-8314-2140> "Raymund Stefancsik")
+
 # Individual: <https://orcid.org/0000-0001-8910-9851> (Lynn Schriml)
 
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q28913673>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0001-8910-9851> "researcher, metadata, diseases, University of Maryland")
@@ -128,11 +135,11 @@ AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wik
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q30032484>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0003-1813-6857> "Canadian biocurator")
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q30032484>) rdfs:label <https://orcid.org/0000-0003-1813-6857> "Pascale Gaudet")
 
-
 # Individual: <https://orcid.org/0000-0003-1834-3856> (Mathias Brochhausen)
 
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q57161944>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0003-1834-3856> "researcher")
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q57161944>) rdfs:label <https://orcid.org/0000-0003-1834-3856> "Mathias Brochhausen")
+
 # Individual: <https://orcid.org/0000-0003-1909-9269> (S. Clint Dowland)
 
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q123250399>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0003-1909-9269> "Researcher ORCID=0000-0003-1909-9269")
@@ -143,6 +150,11 @@ AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wik
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q37377046>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0003-1940-6740> "researcher")
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q37377046>) rdfs:label <https://orcid.org/0000-0003-1940-6740> "Anna Maria Masci")
 
+# Individual: <https://orcid.org/0000-0003-2620-0345> (Asiyah Yu Lin)
+
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q123250403>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0003-2620-0345> "Researcher ORCID=0000-0003-2620-0345")
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q123250403>) rdfs:label <https://orcid.org/0000-0003-2620-0345> "Asiyah Yu Lin")
+
 # Individual: <https://orcid.org/0000-0003-3138-4118> (Jorrit Poelen)
 
 AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q58206618>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0003-3138-4118> "software/data engineer")