Merge pull request #22 from VirtualFlyBrain/release_2025-01-10

release 2025-01-10

.github/workflows/qc.yml

@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.2
+    container: obolibrary/odkfull:v1.5.4
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

imports/merged_import.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/vfbext/imports/merged_import.owl>
-<http://purl.obolibrary.org/obo/vfbext/releases/2024-10-29/imports/merged_import.owl>
-Annotation(owl:versionInfo "2024-10-29")
+<http://purl.obolibrary.org/obo/vfbext/releases/2025-01-10/imports/merged_import.owl>
+Annotation(owl:versionInfo "2025-01-10")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
@@ -47,19 +47,27 @@ Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_00100313>))
 Declaration(Class(<http://purl.obolibrary.org/obo/FBbt_10000000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000005>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000104>))
+Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_10239>))
+Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2>))
+Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2157>))
+Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2759>))
 Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_7227>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000011>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000112>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000659>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000684>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0001479>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0002076>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0002648>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0100026>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0100051>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000125>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001993>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002266>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0010000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0010001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000465>))
+Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000477>))
 Declaration(Class(<http://xmlns.com/foaf/0.1/image>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
@@ -702,14 +710,14 @@ SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000011> <http://purl.obolibrary.
 
 # Class: <http://purl.obolibrary.org/obo/OBI_0000112> (specimen role)
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000112> "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000112> "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen."@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0000112> "specimen role"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000112> <http://purl.obolibrary.org/obo/BFO_0000023>)
 SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000112> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000040> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/OBI_0000312> <http://purl.obolibrary.org/obo/OBI_0000659>))))
 
 # Class: <http://purl.obolibrary.org/obo/OBI_0000659> (specimen collection process)
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000659> "A planned process with the objective of collecting a specimen."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000659> "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed."@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0000659> "specimen collection process")
 EquivalentClasses(<http://purl.obolibrary.org/obo/OBI_0000659> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/OBI_0000011> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/OBI_0000417> <http://purl.obolibrary.org/obo/OBI_0000684>)))
 SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000659> <http://purl.obolibrary.org/obo/OBI_0000011>)
@@ -718,20 +726,41 @@ SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000659> ObjectSomeValuesFrom(<ht
 
 # Class: <http://purl.obolibrary.org/obo/OBI_0000684> (specimen collection objective)
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000684> "A objective specification to obtain a material entity for potential use as an input during an investigation."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0000684> "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed."@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0000684> "specimen collection objective")
 SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000684> <http://purl.obolibrary.org/obo/IAO_0000005>)
 
+# Class: <http://purl.obolibrary.org/obo/OBI_0001479> (specimen from organism)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0001479> "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm)."@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0001479> "specimen from organism")
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBI_0001479> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/OBI_0100051> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/OBI_0000312> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/OBI_0000659> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/OBI_0000293> ObjectUnionOf(<http://purl.obolibrary.org/obo/OBI_0100026> <http://purl.obolibrary.org/obo/UBERON_0000465> <http://purl.obolibrary.org/obo/UBERON_0000477>))))))
+SubClassOf(<http://purl.obolibrary.org/obo/OBI_0001479> <http://purl.obolibrary.org/obo/OBI_0100051>)
+
 # Class: <http://purl.obolibrary.org/obo/OBI_0002076> (collection of specimens)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0002076> "A material entity that has two or more specimens as its parts."@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0002076> "collection of specimens"@en)
 EquivalentClasses(<http://purl.obolibrary.org/obo/OBI_0002076> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000040> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/RO_0002351> <http://purl.obolibrary.org/obo/OBI_0100051>)))
 SubClassOf(<http://purl.obolibrary.org/obo/OBI_0002076> <http://purl.obolibrary.org/obo/BFO_0000040>)
 
+# Class: <http://purl.obolibrary.org/obo/OBI_0002648> (individual organism specimen)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0002648> "A specimen composed of an individual organism to be studied in an investigation."@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0002648> "individual organism specimen")
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBI_0002648> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/OBI_0100051> ObjectExactCardinality(1 <http://purl.obolibrary.org/obo/RO_0002180> <http://purl.obolibrary.org/obo/OBI_0100026>)))
+SubClassOf(<http://purl.obolibrary.org/obo/OBI_0002648> <http://purl.obolibrary.org/obo/OBI_0100051>)
+
+# Class: <http://purl.obolibrary.org/obo/OBI_0100026> (organism)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0100026> "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."@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0100026> "organism"@en)
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBI_0100026> ObjectUnionOf(<http://purl.obolibrary.org/obo/NCBITaxon_10239> <http://purl.obolibrary.org/obo/NCBITaxon_2> <http://purl.obolibrary.org/obo/NCBITaxon_2157> <http://purl.obolibrary.org/obo/NCBITaxon_2759>))
+SubClassOf(<http://purl.obolibrary.org/obo/OBI_0100026> <http://purl.obolibrary.org/obo/BFO_0000040>)
+
 # Class: <http://purl.obolibrary.org/obo/OBI_0100051> (specimen)
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0100051> "A material entity that has the specimen role."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0100051> "A material entity that is collected for potential use as an input upon which measurements or observations are performed."@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0100051> "specimen"@en)
 EquivalentClasses(<http://purl.obolibrary.org/obo/OBI_0100051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000040> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000087> <http://purl.obolibrary.org/obo/OBI_0000112>)))
 SubClassOf(<http://purl.obolibrary.org/obo/OBI_0100051> <http://purl.obolibrary.org/obo/BFO_0000040>)

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for vfbext
 # Generated using ontology-development-kit
-# ODK Version: v1.5.2
+# ODK Version: v1.5.4
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vfbext.Makefile instead
 
@@ -46,7 +46,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.5.2
+ODK_VERSION_MAKEFILE =      v1.5.4
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')