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Merged
XimeAixa merged 2 commits into from
Apr 22, 2026
Merged

Add material entity branch: protein, compound, condensate, and related classes #25

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5fefe59
add material entity to BFO import
XimeAixa Apr 22, 2026
e16f55f
create material entity branch
XimeAixa Apr 22, 2026
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64 changes: 64 additions & 0 deletions src/ontology/idpo-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,14 @@ Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000084>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000085>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000086>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000089>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000091>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000092>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000093>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000094>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000095>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000096>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000097>))
Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000098>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IDPO_0000087>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IDPO_0000088>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000086>))
Expand Down Expand Up @@ -885,6 +893,62 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
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>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000091> (compound)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000091> "A molecule composed of two or more distinct chemical components.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000091> "IDPO:0000091")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000091> "compound")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000091> <http://purl.obolibrary.org/obo/BFO_0000040>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000092> (condensate)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000092> "A compound formed via phase separation or related physicochemical processes.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000092> "IDPO:0000092")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000092> "condensate")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000092> <http://purl.obolibrary.org/obo/IDPO_0000091>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000093> (biomolecular condensate)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000093> "A condensate composed of biomolecules such as proteins, protein regions, or nucleic acid strands, typically formed through phase separation driven by weak multivalent interactions.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000093> "IDPO:0000093")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000093> "biomolecular condensate")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000093> <http://purl.obolibrary.org/obo/IDPO_0000092>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000094> (protein)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000094> "A molecule composed of one or more polypeptide chains.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000094> "IDPO:0000094")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000094> "protein")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000094> <http://purl.obolibrary.org/obo/BFO_0000040>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000095> (protein region)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000095> "A contiguous segment of a protein that can be distinguished by its structural, functional, or sequence properties.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000095> "IDPO:0000095")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000095> "protein region")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000095> <http://purl.obolibrary.org/obo/IDPO_0000094>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000096> (intrinsically disordered protein)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000096> "A protein that wholly lacks a stable, fixed three-dimensional structure under physiological conditions.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000096> "IDPO:0000096")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000096> "intrinsically disordered protein")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000096> <http://purl.obolibrary.org/obo/IDPO_0000094>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000097> (intrinsically disordered region)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000097> "A protein region that lacks a stable, fixed three-dimensional structure under physiological conditions.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000097> "IDPO:0000097")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000097> "intrinsically disordered region")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000097> <http://purl.obolibrary.org/obo/IDPO_0000095>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000098> (ordered region)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000098> "A protein region that adopts a stable, fixed three-dimensional structure under physiological conditions.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000098> "IDPO:0000098")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000098> "ordered region")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000098> <http://purl.obolibrary.org/obo/IDPO_0000095>)


SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/RO_0002233> <http://purl.obolibrary.org/obo/RO_0000086>) <http://purl.obolibrary.org/obo/IDPO_0000088>)
SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/RO_0002234> <http://purl.obolibrary.org/obo/RO_0000086>) <http://purl.obolibrary.org/obo/IDPO_0000087>)
Expand Down
1 change: 1 addition & 0 deletions src/ontology/imports/bfo_terms.txt
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@@ -1,3 +1,4 @@
BFO:0000015
BFO:0000019
BFO:0000034
BFO:0000040
23 changes: 21 additions & 2 deletions src/ontology/imports/merged_import.owl
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Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/idpo/imports/merged_import.owl>
<http://purl.obolibrary.org/obo/idpo/releases/2026-04-21/imports/merged_import.owl>
Annotation(owl:versionInfo "2026-04-21")
<http://purl.obolibrary.org/obo/idpo/releases/2026-04-22/imports/merged_import.owl>
Annotation(owl:versionInfo "2026-04-22")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
Expand All @@ -22,6 +22,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000020>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000023>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000031>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000034>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0003674>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0003824>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0016301>))
Expand Down Expand Up @@ -623,6 +624,24 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.ob
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>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000040> (material entity)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "a flame"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "a forest fire"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "a human being"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "a hurricane"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "a photon"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "a puff of smoke"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "a sea wave"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "a tornado"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "an aggregate of human beings."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "an energy wave"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "an epidemic"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000040> "the undetached arm of a human being"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/BFO_0000040> "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000040> "material entity"@en)
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000040> <http://purl.obolibrary.org/obo/BFO_0000004>)

# Class: <http://purl.obolibrary.org/obo/GO_0003674> (molecular_function)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:pdt") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/GO_0003674> "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.")
Expand Down
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