diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 7667170..187a895 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -140,13 +140,13 @@ AnnotationAssertion(rdfs:label "has final state") ObjectPropertyDomain( ) -ObjectPropertyRange( ) +ObjectPropertyRange( ) # Object Property: (has initial state) AnnotationAssertion(rdfs:label "has initial state") ObjectPropertyDomain( ) -ObjectPropertyRange( ) +ObjectPropertyRange( ) @@ -154,100 +154,102 @@ ObjectPropertyRange( (structural state) +# Class: (protein structural state) -AnnotationAssertion( "A structural property that a protein region can exhibit, defined by its conformational behavior.") +AnnotationAssertion( "A quality of a protein region, defined by its conformational behavior.") AnnotationAssertion( "conformational state") -AnnotationAssertion( "state") +AnnotationAssertion( "structural state") +AnnotationAssertion( "protein structural state") AnnotationAssertion( "IDPO:0000001") -AnnotationAssertion(rdfs:label "structural state") -SubClassOf( ) +AnnotationAssertion(rdfs:label "protein structural state") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) -# Class: (disorder) +# Class: (disorder state) AnnotationAssertion(Annotation( ) Annotation( "PMID:35107780") "Annotation DP04431r001") -AnnotationAssertion(Annotation( "PMID:11910019") "A structural state of a protein region characterized by the absence of a stable, fixed three-dimensional structure, lacking persistent secondary and/or tertiary interactions.") +AnnotationAssertion(Annotation( "PMID:11910019") "A protein structural state of a protein region characterized by the absence of a stable, fixed three-dimensional structure, lacking persistent secondary and/or tertiary interactions.") AnnotationAssertion( "intrinsic disorder") AnnotationAssertion( "structural disorder") AnnotationAssertion( "unstructured") -AnnotationAssertion( "state") +AnnotationAssertion( "protein structural state") AnnotationAssertion( "flexible") AnnotationAssertion( "IDPO:0000002") -AnnotationAssertion(rdfs:label "disorder") +AnnotationAssertion(rdfs:label "disorder state") SubClassOf( ) -# Class: (molten globule) +# Class: (molten globule state) AnnotationAssertion(Annotation( ) Annotation( "PMID:21961597") "Annotation DP01799r004") -AnnotationAssertion(Annotation( "PMID:11910019") "A compact structural state in which a protein region exhibits native-like secondary structure but lacks stable tertiary interactions.") -AnnotationAssertion( "state") +AnnotationAssertion(Annotation( "PMID:11910019") "A type of disorder state in which a protein region exhibits native-like secondary structure but lacks stable tertiary interactions.") +AnnotationAssertion( "protein structural state") AnnotationAssertion( "IDPO:0000003") -AnnotationAssertion(rdfs:label "molten globule") +AnnotationAssertion(rdfs:label "molten globule state") SubClassOf( ) -# Class: (pre-molten globule) +# Class: (pre-molten globule state) AnnotationAssertion(Annotation( ) Annotation( "PMID:20817927") "Annotation DP04101r003") -AnnotationAssertion(Annotation( "PMID:11910019") "A partially condensed state of a protein region characterized by low compactness and the presence of residual or transiently populated secondary structure, often representing an ensemble of rapidly interconverting conformations.") -AnnotationAssertion( "state") +AnnotationAssertion(Annotation( "PMID:11910019") "A type of disorder state in which a protein region exhibits low compactness and residual or transiently populated secondary structure, representing an ensemble of rapidly interconverting conformations.") +AnnotationAssertion( "protein structural state") AnnotationAssertion( "IDPO:0000004") -AnnotationAssertion(rdfs:label "pre-molten globule") +AnnotationAssertion(rdfs:label "pre-molten globule state") SubClassOf( ) -# Class: (random coil) +# Class: (random coil state) -AnnotationAssertion( "A highly extended and dynamic conformational state of intrinsically disordered proteins with minimal compaction, lacking stable secondary or tertiary structure and maintained by high net charge.") +AnnotationAssertion( "A type of disorder state in which a protein region exhibits maximal conformational extension and minimal compaction, lacking stable secondary and tertiary structure.") AnnotationAssertion( "PMID:36368411") AnnotationAssertion( "native coil") -AnnotationAssertion( "state") +AnnotationAssertion( "protein structural state") AnnotationAssertion( "IDPO:0000005") -AnnotationAssertion(rdfs:label "random coil") +AnnotationAssertion(rdfs:label "random coil state") SubClassOf( ) -# Class: (order) +# Class: (order state) AnnotationAssertion(Annotation( ) Annotation( "PMID:29499137") "Annotation DP04243r003") -AnnotationAssertion(Annotation(rdfs:comment "PMID:11910019") "A structural state of a protein region in which atoms are arranged in a stable, well-defined three-dimensional conformation, including persistent secondary and tertiary structure.") +AnnotationAssertion(Annotation(rdfs:comment "PMID:11910019") "A protein structural state of a protein region in which atoms are arranged in a stable, well-defined three-dimensional conformation, including persistent secondary and tertiary structure.") AnnotationAssertion( "structural order") AnnotationAssertion( "structured state") AnnotationAssertion( "folded state") AnnotationAssertion( "globular conformation") -AnnotationAssertion( "state") +AnnotationAssertion( "protein structural state") AnnotationAssertion( "IDPO:0000006") -AnnotationAssertion(rdfs:label "order") +AnnotationAssertion(rdfs:label "order state") SubClassOf( ) -# Class: (structurally undefined) +# Class: (structurally undefined state) -AnnotationAssertion( "A structural classification for a protein region for which a definitive structural state cannot be determined, due to insufficient or ambiguous evidence.") +AnnotationAssertion( "A protein structural state of a protein region for which a definitive structural state cannot be determined, due to insufficient or ambiguous evidence.") AnnotationAssertion( "structural state not defined") AnnotationAssertion( "undefined structural state") -AnnotationAssertion( "state") +AnnotationAssertion( "protein structural state") AnnotationAssertion( "inconclusive structural state") AnnotationAssertion( "indeterminate structural state") AnnotationAssertion( "IDPO:0000007") -AnnotationAssertion(rdfs:label "structurally undefined") +AnnotationAssertion(rdfs:label "structurally undefined state") SubClassOf( ) -# Class: (likely order) +# Class: (likely order state) -AnnotationAssertion( "A structural classification for a protein region for which a definitive structural state cannot be determined, yet available data suggest it is ordered.") +AnnotationAssertion( "A structurally undefined state of a protein region for which a definitive structural state cannot be determined, yet available data suggest it is ordered.") AnnotationAssertion( "PMID:38519511") AnnotationAssertion( "presumed order") AnnotationAssertion( "probably order") -AnnotationAssertion( "state") +AnnotationAssertion( "protein structural state") AnnotationAssertion( "IDPO:0000008") -AnnotationAssertion(rdfs:label "likely order") +AnnotationAssertion(rdfs:label "likely order state") SubClassOf( ) -# Class: (likely disorder) +# Class: (likely disorder state) -AnnotationAssertion( "A structural classification for a protein region for which a definitive structural state cannot be determined, yet available data suggest it is disordered.") +AnnotationAssertion( "A structurally undefined state of a protein region for which a definitive structural state cannot be determined, yet available data suggest it is disordered.") AnnotationAssertion( "presumed disorder") AnnotationAssertion( "probably disorder") -AnnotationAssertion( "state") +AnnotationAssertion( "protein structural state") AnnotationAssertion( "IDPO:0000009") -AnnotationAssertion(rdfs:label "likely disorder") +AnnotationAssertion(rdfs:label "likely disorder state") SubClassOf( ) # Class: (structural transition) @@ -774,52 +776,54 @@ AnnotationAssertion( "amorphous aggregate formation") SubClassOf( ) -# Class: (material state) +# Class: (condensate material state) -AnnotationAssertion(Annotation( "PMID:29602697") "A physical property of a biomolecular assembly that describes its viscoelastic behavior and internal molecular organization under given conditions, used to characterize proteins or protein regions that are part of the condensate.") +AnnotationAssertion(Annotation( "PMID:29602697") "A quality that describes the viscoelastic behavior and internal molecular organization of a condensate under given conditions, used to characterize proteins or protein regions that are part of the condensate.") AnnotationAssertion( "physical state") -AnnotationAssertion( "state") +AnnotationAssertion( "material state") +AnnotationAssertion( "condensate material state") AnnotationAssertion( "IDPO:0000075") -AnnotationAssertion(rdfs:label "material state") -SubClassOf( ) +AnnotationAssertion(rdfs:label "condensate material state") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) -# Class: (liquid-like state) +# Class: (liquid-like condensate state) -AnnotationAssertion(Annotation( "PMID:33510441") "A state characterized by dynamic fusion, fission, dripping behavior, and rapid internal molecular rearrangements. Often represents the initial phase-separated state with high internal mobility and exchange rates.") +AnnotationAssertion(Annotation( "PMID:33510441") "A condensate state characterized by dynamic fusion, fission, dripping behavior, and rapid internal molecular rearrangements.") AnnotationAssertion( "PMID:38287572") -AnnotationAssertion( "state") +AnnotationAssertion( "condensate material state") AnnotationAssertion( "liquid-like condensate") AnnotationAssertion( "IDPO:0000076") -AnnotationAssertion(rdfs:label "liquid-like state") +AnnotationAssertion(rdfs:label "liquid-like condensate state") SubClassOf( ) -# Class: (gel-like state) +# Class: (gel-like condensate state) -AnnotationAssertion(Annotation( "PMID:33510441") "A viscoelastic state with physical crosslinks between components, showing partial solid-like behavior while retaining some molecular mobility. Often arises through gelation processes.") +AnnotationAssertion(Annotation( "PMID:33510441") "A condensate state characterized by physical crosslinks between components, showing partial solid-like behavior while retaining some molecular mobility.") AnnotationAssertion( "PMID:34102212") -AnnotationAssertion( "state") +AnnotationAssertion( "condensate material state") AnnotationAssertion( "gel-like condensate") AnnotationAssertion( "IDPO:0000077") -AnnotationAssertion(rdfs:label "gel-like state") +AnnotationAssertion(rdfs:label "gel-like condensate state") SubClassOf( ) -# Class: (glass-like state) +# Class: (glass-like condensate state) -AnnotationAssertion(Annotation( "PMID:33510441") "A metastable, non-crystalline state with gradually evolving mechanical properties and no characteristic timescale for structural solidification. Formed via a glass transition process.") -AnnotationAssertion( "state") +AnnotationAssertion(Annotation( "PMID:33510441") "A condensate state characterized by gradually evolving mechanical properties, an absence of crystalline order, and no characteristic timescale for structural solidification.") +AnnotationAssertion( "condensate material state") AnnotationAssertion( "glass-like condensate") AnnotationAssertion( "IDPO:0000078") -AnnotationAssertion(rdfs:label "glass-like state") +AnnotationAssertion(rdfs:label "glass-like condensate state") SubClassOf( ) -# Class: (solid-like state) +# Class: (solid-like condensate state) -AnnotationAssertion(Annotation( "PMID:33510441") "A rigid state with minimal internal molecular motion, typically arising through irreversible interactions or pathological ageing processes such as amyloid formation.") +AnnotationAssertion(Annotation( "PMID:33510441") "A condensate state characterized by minimal internal molecular motion, typically arising through irreversible interactions or pathological ageing processes such as amyloid formation.") AnnotationAssertion( "PMID:34095780") -AnnotationAssertion( "state") +AnnotationAssertion( "condensate material state") AnnotationAssertion( "solid-like condensate") AnnotationAssertion( "IDPO:0000079") -AnnotationAssertion(rdfs:label "solid-like state") +AnnotationAssertion(rdfs:label "solid-like condensate state") SubClassOf( ) # Class: (transition) @@ -829,7 +833,6 @@ AnnotationAssertion( "IDPO:0000080") AnnotationAssertion(rdfs:label "transition") SubClassOf( ) -DisjointClasses( ) # Class: (transition to a more ordered state) @@ -885,13 +888,13 @@ AnnotationAssertion( "post-translational modification motif") SubClassOf( ) -# Class: (state) +# Class: (DEPRECATED state) -AnnotationAssertion( "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.") -AnnotationAssertion( "state") -AnnotationAssertion( "IDPO:0000089") -AnnotationAssertion(rdfs:label "state") -SubClassOf( ) +AnnotationAssertion(rdfs:comment "The term was originally introduced as a high-level grouping class but is now obsolete because it is overly general and semantically ambiguous.") +AnnotationAssertion(rdfs:label "DEPRECATED state") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Class: (compound)