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Merged
XimeAixa merged 3 commits into from
Sep 29, 2025
Merged

Add BFO roots for structural state and structural transition #11

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f5a8793
Update bfo_terms.txt
cthoyt Sep 25, 2025
c0c93b0
Update idpo-edit.owl
cthoyt Sep 26, 2025
6f6d14d
Update imports
cthoyt Sep 26, 2025
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2 changes: 2 additions & 0 deletions src/ontology/idpo-edit.owl
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Expand Up @@ -841,6 +841,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000080> "transition")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000080> "IDPO:0000080")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000080> "transition")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000080> <http://purl.obolibrary.org/obo/BFO_0000015>)
DisjointClasses(<http://purl.obolibrary.org/obo/IDPO_0000080> <http://purl.obolibrary.org/obo/IDPO_0000089>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000081> (transition to a more ordered state)
Expand Down Expand Up @@ -902,6 +903,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000089> "state")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000089> "IDPO:0000089")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000089> "state")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000089> <http://purl.obolibrary.org/obo/BFO_0000019>)


SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/RO_0002233> <http://purl.obolibrary.org/obo/RO_0000086>) <http://purl.obolibrary.org/obo/IDPO_0000088>)
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56 changes: 54 additions & 2 deletions src/ontology/imports/bfo_import.owl
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Expand Up @@ -7,13 +7,17 @@ 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/2025-09-10/imports/bfo_import.owl>
<http://purl.obolibrary.org/obo/idpo/releases/2025-09-26/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 "2025-09-10")
Annotation(owl:versionInfo "2025-09-26")

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_0000019>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000020>))
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.org/dc/elements/1.1/source>))
Expand All @@ -22,6 +26,10 @@ Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
# Annotation Properties
############################

# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000112> (example of usage)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000112> "example of usage"@en)

# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000115> (definition)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000115> "definition"@en)
Expand All @@ -38,17 +46,61 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000119> "def

# Class: <http://purl.obolibrary.org/obo/BFO_0000001> (entity)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000001> "Julius Caesar"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000001> "Verdi’s Requiem"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000001> "the Second World War"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000001> "your body mass index"@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000001> "entity"@en)

# Class: <http://purl.obolibrary.org/obo/BFO_0000002> (continuant)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000002> "continuant"@en)
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000002> <http://purl.obolibrary.org/obo/BFO_0000001>)
DisjointClasses(<http://purl.obolibrary.org/obo/BFO_0000002> <http://purl.obolibrary.org/obo/BFO_0000003>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000003> (occurrent)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000003> "occurrent"@en)
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000003> <http://purl.obolibrary.org/obo/BFO_0000001>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000015> (process)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000015> "a process of cell-division, \\ a beating of the heart"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000015> "a process of meiosis"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000015> "a process of sleeping"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000015> "the course of a disease"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000015> "the flight of a bird"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000015> "the life of an organism"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000015> "your process of aging."@en)
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_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)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000019> "the color of a tomato"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000019> "the length of the circumference of your waist"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000019> "the mass of this piece of gold."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000019> "the shape of your nose"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000019> "the shape of your nostril"@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000019> "quality"@en)
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000019> <http://purl.obolibrary.org/obo/BFO_0000020>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000020> (specifically dependent continuant)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "of one-sided specifically dependent continuants: the mass of this tomato"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "the disposition of this fish to decay"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "the function of this heart: to pump blood"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "the pink color of a medium rare piece of grilled filet mignon at its center"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "the role of being a doctor"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "the shape of this hole."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000020> "the smell of this portion of mozzarella"@en)
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>)


)
1 change: 1 addition & 0 deletions src/ontology/imports/bfo_terms.txt
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@@ -1 +1,2 @@
BFO:0000015
BFO:0000019
20 changes: 18 additions & 2 deletions src/ontology/imports/omo_import.owl
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Expand Up @@ -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/2025-09-10/imports/omo_import.owl>
<http://purl.obolibrary.org/obo/idpo/releases/2025-09-26/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 "2025-09-10")
Annotation(owl:versionInfo "2025-09-26")

Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000027>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000030>))
Expand All @@ -36,20 +36,28 @@ Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000423>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000428>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/OMO_0001000>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/OMO_0001002>))
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.org/dc/elements/1.1/source>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>))
############################
# Annotation Properties
############################

# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000112> (example of usage)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000112> "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0000112> "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>"@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000112> "example of usage"@en)

# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000115> (definition)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000115> "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en)
Expand All @@ -73,6 +81,13 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000700> "has
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.")
AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> "has broad synonym"@en)

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (has cross-reference)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://orcid.org/0000-0002-7356-1779>)
AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "has cross-reference")

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> (has exact synonym)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.")
Expand Down Expand Up @@ -127,6 +142,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000225> <http://purl.obolibrary.

# Class: <http://purl.obolibrary.org/obo/IAO_0000409> (denotator type)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/IAO_0000409> "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000409> "A denotator type indicates how a term should be interpreted from an ontological perspective."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0000409> "Barry Smith, Werner Ceusters"@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000409> "denotator type"@en)
Expand Down
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