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Merge pull request #34 from BioComputingUP/feat/new-glyco-terms
New glycosylation terms added + pre release cleanup (2026/07/07)
2 parents 3d97616 + e1e8703 commit eb5263b

3 files changed

Lines changed: 54 additions & 16 deletions

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‎src/ontology/idpo-edit.owl‎

Lines changed: 42 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -105,6 +105,8 @@ Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000097>))
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Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000098>))
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Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000099>))
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Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000100>))
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Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000101>))
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Declaration(Class(<http://purl.obolibrary.org/obo/IDPO_0000102>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IDPO_0000087>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IDPO_0000088>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000086>))
@@ -119,6 +121,7 @@ Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
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Declaration(AnnotationProperty(<http://purl.org/dc/terms/description>))
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Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
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Declaration(AnnotationProperty(<http://purl.org/dc/terms/title>))
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Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#consider>))
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Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#default-namespace>))
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Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>))
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Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
@@ -134,6 +137,10 @@ Declaration(AnnotationProperty(rdfs:label))
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# Annotation Properties
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############################
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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#consider> (consider)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#consider> "consider")
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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> (has_obo_namespace)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> "has_obo_namespace")
@@ -145,12 +152,14 @@ AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#has
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# Object Property: <http://purl.obolibrary.org/obo/IDPO_0000087> (has final state)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000087> "A relation between a process and a quality that inheres in a participant of the process at the temporal end of that process.")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000087> "has final state")
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ObjectPropertyDomain(<http://purl.obolibrary.org/obo/IDPO_0000087> <http://purl.obolibrary.org/obo/BFO_0000015>)
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ObjectPropertyRange(<http://purl.obolibrary.org/obo/IDPO_0000087> <http://purl.obolibrary.org/obo/BFO_0000019>)
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# Object Property: <http://purl.obolibrary.org/obo/IDPO_0000088> (has initial state)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000088> "A relation between a process and a quality that inheres in a participant of the process at the temporal beginning of that process.")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000088> "has initial state")
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ObjectPropertyDomain(<http://purl.obolibrary.org/obo/IDPO_0000088> <http://purl.obolibrary.org/obo/BFO_0000015>)
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ObjectPropertyRange(<http://purl.obolibrary.org/obo/IDPO_0000088> <http://purl.obolibrary.org/obo/BFO_0000019>)
@@ -390,7 +399,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000022> ObjectSomeValuesFrom(<h
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000023> (pre-molten globule to molten globule)
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AnnotationAssertion(Annotation(<http://purl.org/dc/elements/1.1/source> <https://disprot.org/DP00015r024>) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:32338601") <http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/IDPO_0000023> "Annotation DP00015r024")
393-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000023> "A structural transition in which a protein region changes from a pre-molten glouble state to a molten globule state, by gaining native-like secondary structure elements.")
402+
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000023> "A structural transition in which a protein region changes from a pre-molten globule state to a molten globule state, by gaining native-like secondary structure elements.")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000023> "protein_structural_transition")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000023> "IDPO:0000023")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000023> "pre-molten globule to molten globule")
@@ -465,7 +474,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000029> ObjectSomeValuesFrom(<h
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000030> (entropic chain function)
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AnnotationAssertion(Annotation(<http://purl.obolibrary.org/obo/IAO_0000119> "PMID:12022860") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000030> "A disorder function that is either mechanical or regulatory and enabled by the dynamic conformational flexibility of an intrincally disordered protein region that lacks a stable tertiary structure.")
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AnnotationAssertion(Annotation(<http://purl.obolibrary.org/obo/IAO_0000119> "PMID:12022860") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000030> "A disorder function that is either mechanical or regulatory and enabled by the dynamic conformational flexibility of an intrinsically disordered protein region that lacks a stable tertiary structure.")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000030> "entropic chain")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/IDPO_0000030> "entropic bristle")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/IDPO_0000030> "entropic clock")
@@ -567,10 +576,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000040> <http://purl.obolibrary
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000041> (glycosylation target role)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000041> "A post-translational modification target role role that inheres in an intrinsically disordered protein region in virtue of its recognition by a glycosyltransferase, and is realized in the covalent addition of a sugar moiety to that region.")
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000041> "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by a glycosylation machinery, and is realized in the covalent addition of a sugar moiety to that region.")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000041> "glycosylation display site")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/IDPO_0000041> "N-linked glycosylation site")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/IDPO_0000041> "O-linked glycosylation site")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000041> "disorder_role")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000041> "IDPO:0000041")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000041> "glycosylation target role")
@@ -860,12 +867,13 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000079> "solid-like condensate state")
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SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000079> <http://purl.obolibrary.org/obo/IDPO_0000075>)
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000080> (DEPRECATED transition)
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000080> (obsolete transition)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000080> "OBSOLETE. A temporally extended process in which a protein or protein region changes from one state to another, under specific conditions.")
873+
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/IDPO_0000080> <http://purl.obolibrary.org/obo/IDPO_0000010>)
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/IDPO_0000080> <http://purl.obolibrary.org/obo/IDPO_0000083>)
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AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IDPO_0000080> "Obsolete due to semantic ambiguity and excessive generality.")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000080> "DEPRECATED transition")
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AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/IDPO_0000080> <http://purl.obolibrary.org/obo/IDPO_0000010>)
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AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/IDPO_0000080> <http://purl.obolibrary.org/obo/IDPO_0000083>)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000080> "obsolete transition")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/IDPO_0000080> "true"^^xsd:boolean)
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000081> (transition to a more ordered state)
@@ -923,12 +931,13 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000086> "post-translational modification motif role")
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SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000086> <http://purl.obolibrary.org/obo/IDPO_0000036>)
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000089> (DEPRECATED state)
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000089> (obsolete state)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000089> "OBSOLETE. A quality of a protein or protein region that describes its organization, conformation, or material properties at a given time, under specific conditions, and that can change dynamically.")
937+
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/IDPO_0000089> <http://purl.obolibrary.org/obo/IDPO_0000001>)
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/IDPO_0000089> <http://purl.obolibrary.org/obo/IDPO_0000075>)
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AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IDPO_0000089> "The term was originally introduced as a high-level grouping class but is now obsolete because it is overly general and semantically ambiguous.")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000089> "DEPRECATED state")
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AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/IDPO_0000089> <http://purl.obolibrary.org/obo/IDPO_0000001>)
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AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/IDPO_0000089> <http://purl.obolibrary.org/obo/IDPO_0000075>)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000089> "obsolete state")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/IDPO_0000089> "true"^^xsd:boolean)
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000091> (compound)
@@ -1015,6 +1024,26 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000100> "di
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SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000100> <http://purl.obolibrary.org/obo/BFO_0000023>)
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SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000100> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000081> <http://purl.obolibrary.org/obo/IDPO_0000095>))
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000101> (N-glycosylation target role)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000101> "A glycosylation target role that inheres in an intrinsically disordered protein region in virtue of its recognition by an N-glycosylation machinery, and is realized in the covalent addition of a sugar moiety to a nitrogen atom of an amino acid side chain in that region.")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000101> "N-glycosylation display site")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000101> "N-linked glycosylation target role")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000101> "disorder_role")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000101> "IDPO:0000101")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000101> "N-glycosylation target role")
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SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000101> <http://purl.obolibrary.org/obo/IDPO_0000041>)
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# Class: <http://purl.obolibrary.org/obo/IDPO_0000102> (O-glycosylation target role)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000102> "A glycosylation target role that inheres in an intrinsically disordered protein region in virtue of its recognition by an O-glycosylation machinery, and is realized in the covalent addition of a sugar moiety to an oxygen atom of an amino acid side chain in that region.")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000102> "O-glycosylation display site")
1041+
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IDPO_0000102> "O-linked glycosylation target role")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000102> "disorder_role")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000102> "IDPO:0000102")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000102> "O-glycosylation target role")
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SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000102> <http://purl.obolibrary.org/obo/IDPO_0000041>)
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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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SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/RO_0002234> <http://purl.obolibrary.org/obo/RO_0000086>) <http://purl.obolibrary.org/obo/IDPO_0000087>)

‎src/ontology/imports/iao_terms.txt‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1 +1,2 @@
1-
IAO:0000030
1+
IAO:0000030
2+
IAO:0100001

‎src/ontology/imports/merged_import.owl‎

Lines changed: 10 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
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Ontology(<http://purl.obolibrary.org/obo/idpo/imports/merged_import.owl>
10-
<http://purl.obolibrary.org/obo/idpo/releases/2026-05-14/imports/merged_import.owl>
11-
Annotation(owl:versionInfo "2026-05-14")
10+
<http://purl.obolibrary.org/obo/idpo/releases/2026-07-07/imports/merged_import.owl>
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Annotation(owl:versionInfo "2026-07-07")
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
@@ -101,12 +101,14 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000112>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000700>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OMO_0003000>))
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Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
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Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
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Declaration(AnnotationProperty(<http://purl.org/dc/terms/description>))
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Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
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Declaration(AnnotationProperty(<http://purl.org/dc/terms/title>))
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Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#consider>))
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Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#default-namespace>))
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Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>))
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Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
@@ -146,6 +148,12 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000119> "def
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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)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000700> "has ontology root term"@en)
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# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0100001> (term replaced by)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0100001> "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0100001> "Person:Alan Ruttenberg"@en)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0100001> "term replaced by"@en)
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# Annotation Property: <http://purl.obolibrary.org/obo/OMO_0003000> (abbreviation)
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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)")

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