Merge pull request #18 from BioComputingUP/BFO-roots

BFO root added for disorder function

Author: XimeAixa

src/ontology/idpo-edit.owl

@@ -480,6 +480,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000029> "disorder_function")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000029> "IDPO:0000029")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000029> "disorder function")
+SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000029> <http://purl.obolibrary.org/obo/BFO_0000034>)
 
 # Class: <http://purl.obolibrary.org/obo/IDPO_0000030> (entropic chain)
 
@@ -785,8 +786,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000065> ObjectSomeValuesFrom(<h
 AnnotationAssertion(Annotation(<http://purl.obolibrary.org/obo/IAO_0000119> "PMID:33510441") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000066> "Process involving a non-native state of a protein in which isoluble intermolecular interactions are established to form a higher-order irreversible assembly, usually as result of aberrant liquid-liquid phase separation.")
 AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/IDPO_0000066> <https://orcid.org/0000-0001-8042-9939>)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/IDPO_0000066> "PMID:38825008")
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000066> "aggregate formation")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000066> "aggregate assembly")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000066> "aggregate formation")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000066> "protein aggregation")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000066> "transition")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000066> "IDPO:0000066")

src/ontology/imports/bfo_import.owl

@@ -7,16 +7,19 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/idpo/imports/bfo_import.owl>
-<http://purl.obolibrary.org/obo/idpo/releases/2025-09-26/imports/bfo_import.owl>
+<http://purl.obolibrary.org/obo/idpo/releases/2025-09-30/imports/bfo_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl>)
-Annotation(owl:versionInfo "2025-09-26")
+Annotation(owl:versionInfo "2025-09-30")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
+Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
+Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000017>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000019>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000020>))
+Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000034>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000112>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
@@ -75,6 +78,26 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.ob
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000015> "process"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000015> <http://purl.obolibrary.org/obo/BFO_0000003>)
 
+# Class: <http://purl.obolibrary.org/obo/BFO_0000016> (disposition)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000016> "an atom of element X has the disposition to decay to an atom of element Y"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000016> "certain people have a predisposition to colon cancer"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000016> "children are innately disposed to categorize objects in certain ways."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000016> "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000016> "disposition"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000016> <http://purl.obolibrary.org/obo/BFO_0000017>)
+
+# Class: <http://purl.obolibrary.org/obo/BFO_0000017> (realizable entity)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000017> "the disposition of this piece of metal to conduct electricity."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000017> "the disposition of your blood to coagulate"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000017> "the function of your reproductive organs"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000017> "the role of being a doctor"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000017> "the role of this boundary to delineate where Utah and Colorado meet"@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000017> "realizable entity"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000017> <http://purl.obolibrary.org/obo/BFO_0000020>)
+DisjointClasses(<http://purl.obolibrary.org/obo/BFO_0000017> <http://purl.obolibrary.org/obo/BFO_0000019>)
+
 # Class: <http://purl.obolibrary.org/obo/BFO_0000019> (quality)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000019> "the ambient temperature of this portion of air"@en)
@@ -102,5 +125,13 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.ob
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000020> "specifically dependent continuant"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000020> <http://purl.obolibrary.org/obo/BFO_0000002>)
 
+# Class: <http://purl.obolibrary.org/obo/BFO_0000034> (function)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000034> "the function of a hammer to drive in nails"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000034> "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000034> "the function of amylase in saliva to break down starch into sugar"@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000034> "function"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000034> <http://purl.obolibrary.org/obo/BFO_0000016>)
+
 
 )

src/ontology/imports/bfo_terms.txt

@@ -1,2 +1,3 @@
 BFO:0000015
 BFO:0000019
+BFO:0000034

src/ontology/imports/omo_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/idpo/imports/omo_import.owl>
-<http://purl.obolibrary.org/obo/idpo/releases/2025-09-26/imports/omo_import.owl>
+<http://purl.obolibrary.org/obo/idpo/releases/2025-09-30/imports/omo_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/omo/releases/2025-06-18/omo.owl>)
-Annotation(owl:versionInfo "2025-09-26")
+Annotation(owl:versionInfo "2025-09-30")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000027>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000030>))
@@ -40,6 +40,7 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000112>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000700>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OMO_0003000>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
@@ -76,6 +77,13 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000119> "def
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000700> "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."@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000700> "has ontology root term"@en)
 
+# Annotation Property: <http://purl.obolibrary.org/obo/OMO_0003000> (abbreviation)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/OMO_0003000> "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OMO_0003000> "A synonym type for describing abbreviations or initalisms")
+AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OMO_0003000> <https://orcid.org/0000-0003-4423-4370>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OMO_0003000> "abbreviation")
+
 # Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> (has broad synonym)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.")

src/ontology/imports/omo_terms.txt

@@ -0,0 +1 @@
+OMO:0003000

src/ontology/imports/ro_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/idpo/imports/ro_import.owl>
-<http://purl.obolibrary.org/obo/idpo/releases/2025-09-26/imports/ro_import.owl>
+<http://purl.obolibrary.org/obo/idpo/releases/2025-09-30/imports/ro_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ro/releases/2025-06-24/ro.owl>)
-Annotation(owl:versionInfo "2025-09-26")
+Annotation(owl:versionInfo "2025-09-30")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))

src/ontology/imports/ro_terms.txt

@@ -1,3 +1,4 @@
 RO:0000086
+RO:0000056
 RO:0002233
 RO:0002234