diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 187a895..2fd28c3 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -139,13 +139,13 @@ AnnotationAssertion(rdfs:label (has final state) AnnotationAssertion(rdfs:label "has final state") -ObjectPropertyDomain( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (has initial state) AnnotationAssertion(rdfs:label "has initial state") -ObjectPropertyDomain( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -252,21 +252,22 @@ AnnotationAssertion( "likely disorder state") SubClassOf( ) -# Class: (structural transition) +# Class: (protein structural transition) AnnotationAssertion( "A dynamic process in which a protein region undergoes a reversible or irreversible transformation between defined structural states.") AnnotationAssertion( "conformational transition") -AnnotationAssertion( "transition") +AnnotationAssertion( "structural transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000010") -AnnotationAssertion(rdfs:label "structural transition") -SubClassOf( ) +AnnotationAssertion(rdfs:label "protein structural transition") +SubClassOf( ) # Class: (disorder to order) AnnotationAssertion(Annotation( ) Annotation( "PMID:38801244") "Annotation DP04243r004") AnnotationAssertion( "A structural transition in which a protein region changes from a disordered state to a fully ordered, well-defined three-dimensional conformation.") AnnotationAssertion( "structural ordering") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000011") AnnotationAssertion(rdfs:label "disorder to order") SubClassOf( ) @@ -277,7 +278,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:24356903") "Annotation DP01511r002") AnnotationAssertion( "A structural transition in which a protein changes from a molten globule state to a fully ordered, well-defined three-dimensional conformation.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000012") AnnotationAssertion(rdfs:label "molten globule to order") SubClassOf( ) @@ -288,7 +289,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:23462742") "Annotation DP02342r013") AnnotationAssertion( "A structural transition in which a protein region changes from a pre-molten globule to a fully ordered, well-defined three-dimensional conformation.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000013") AnnotationAssertion(rdfs:label "pre-molten globule to order") SubClassOf( ) @@ -300,7 +301,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:32817423") "Annotation DP03670r005") AnnotationAssertion( "A structural transition in which a protein region changes from an ordered state to a fully disordered conformation, losing secondary and tertiary structure elements.") AnnotationAssertion( "structural unfolding") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000014") AnnotationAssertion(rdfs:label "order to disorder") SubClassOf( ) @@ -310,7 +311,7 @@ SubClassOf( ObjectSomeValuesFrom( (order to molten globule) AnnotationAssertion( "A structural transition in which a protein region changes from an ordered state to a molten globule state, losing specific tertiary interactions while retaining native-like secondary structure.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000015") AnnotationAssertion(rdfs:label "order to molten globule") SubClassOf( ) @@ -320,7 +321,7 @@ SubClassOf( ObjectSomeValuesFrom( (order to pre-molten globule) AnnotationAssertion( "A structural transition in which a protein region changes from an ordered state to a pre-molten globule state, losing stable tertiary and secondary interactions and retaining only residual secondary structure elements.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000016") AnnotationAssertion(rdfs:label "order to pre-molten globule") SubClassOf( ) @@ -331,7 +332,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:29136196") "Annotation DP00207r012") AnnotationAssertion( "A structural transition in which a protein region changes from a disordered state to a molten globule state, by gaining native-like secondary structure elements.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000018") AnnotationAssertion(rdfs:label "disorder to molten globule") SubClassOf( ) @@ -342,7 +343,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:36037701") "Annotation DP03773r003") AnnotationAssertion( "A structural transition in which a protein region changes from a disordered state to a pre-molten globule state, by gaining residual or transiently populated secondary structure elements.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000019") AnnotationAssertion(rdfs:label "disorder to pre-molten globule") SubClassOf( ) @@ -352,7 +353,7 @@ SubClassOf( ObjectSomeValuesFrom( (molten globule to disorder) AnnotationAssertion( "A structural transition in which a protein region changes from a molten globule state to a fully disordered state, losing all secondary structure elements.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000020") AnnotationAssertion(rdfs:label "molten globule to disorder") SubClassOf( ) @@ -362,7 +363,7 @@ SubClassOf( ObjectSomeValuesFrom( (molten globule to pre-molten globule) AnnotationAssertion( "A structural transition in which a protein region changes from a molten globule state to a pre-molten globule state, losing native-like secondary structure, maintaining only residual secondary structure elements.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000021") AnnotationAssertion(rdfs:label "molten globule to pre-molten globule") SubClassOf( ) @@ -372,7 +373,7 @@ SubClassOf( ObjectSomeValuesFrom( (pre-molten globule to disorder) AnnotationAssertion( "A structural transition in which a protein region changes from a pre-molten globule state to a disordered state, losing residual or transiently populated secondary structure.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000022") AnnotationAssertion(rdfs:label "pre-molten globule to disorder") SubClassOf( ) @@ -383,7 +384,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:32338601") "Annotation DP00015r024") AnnotationAssertion( "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.") -AnnotationAssertion( "transition") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000023") AnnotationAssertion(rdfs:label "pre-molten globule to molten globule") SubClassOf( ) @@ -392,12 +393,12 @@ SubClassOf( ObjectSomeValuesFrom( (liquid-liquid phase separation) -AnnotationAssertion(Annotation( "PMID:29602697") "A demixing phenomenon driven by weak, transient multivalent interactions, resulting in two separate liquid phases, a dense phase and a dilute phase, that then stably coexist.") +AnnotationAssertion(Annotation( "PMID:29602697") "A biomolecular condensate formation involving a demixing driven by weak, transient multivalent interactions, resulting in two separate liquid phases, a dense phase and a dilute phase, that then stably coexist.") AnnotationAssertion( ) AnnotationAssertion( "PMID:38287572") AnnotationAssertion(Annotation( ) "LLPS") AnnotationAssertion( "liquid–liquid demixing") -AnnotationAssertion( "transition") +AnnotationAssertion( "higher-order assembly transition") AnnotationAssertion( "IDPO:0000025") AnnotationAssertion(rdfs:label "liquid-liquid phase separation") SubClassOf( ) @@ -406,12 +407,12 @@ SubClassOf( ObjectSomeValuesFrom( (condensate ageing) -AnnotationAssertion(Annotation( "PMID:33510441") "A time-dependent process in which biomolecular condensates progressively transition from a dynamic, liquid-like state to less dynamic gel-like, glass-like, or solid-like states.") +AnnotationAssertion(Annotation( "PMID:33510441") "A higher-order assembly transition in which biomolecular condensates progressively transition from a dynamic, liquid-like state to less dynamic gel-like, glass-like, or solid-like states.") AnnotationAssertion( ) AnnotationAssertion( "PMID:29358076") AnnotationAssertion( "condensate hardening") AnnotationAssertion( "condensate maturation") -AnnotationAssertion( "transition") +AnnotationAssertion( "higher-order assembly transition") AnnotationAssertion( "IDPO:0000026") AnnotationAssertion(rdfs:label "condensate ageing") SubClassOf( ) @@ -419,12 +420,12 @@ SubClassOf( ObjectSomeValuesFrom( (gelation) -AnnotationAssertion(Annotation( "PMID:29602697") "A physical process by which a liquid-like condensate transitions into a viscoelastic, crosslinked gel-like state, driven by increased concentration or multivalent interactions.") +AnnotationAssertion(Annotation( "PMID:29602697") "A higher-order assembly transition by which a liquid-like condensate transitions into a viscoelastic, crosslinked gel-like state, driven by increased concentration or multivalent interactions.") AnnotationAssertion( ) AnnotationAssertion( "PMID:22579281") AnnotationAssertion( "liquid to gel transition") AnnotationAssertion( "condensate gelation") -AnnotationAssertion( "transition") +AnnotationAssertion( "higher-order assembly transition") AnnotationAssertion( "IDPO:0000027") AnnotationAssertion(rdfs:label "gelation") SubClassOf( ) @@ -433,11 +434,11 @@ SubClassOf( ObjectSomeValuesFrom( (crystallization) -AnnotationAssertion(Annotation( "PMID:29602697") "A physical process through which a disordered liquid state transitions into a more ordered glass-like state, characterized by slow relaxation and arrested molecular motion.") +AnnotationAssertion(Annotation( "PMID:29602697") "A higher-order assembly transition through which a disordered liquid state transitions into a more ordered glass-like state, characterized by slow relaxation and arrested molecular motion.") AnnotationAssertion( ) AnnotationAssertion( "liquid to glass transition") AnnotationAssertion( "condensate crystallization") -AnnotationAssertion( "transition") +AnnotationAssertion( "higher-order assembly transition") AnnotationAssertion( "IDPO:0000028") AnnotationAssertion(rdfs:label "crystallization") SubClassOf( ) @@ -755,23 +756,23 @@ SubClassOf( ObjectSomeValuesFrom( (protein aggregate formation) -AnnotationAssertion(Annotation( "PMID:33510441") "Process involving a non-native state of a protein in which insoluble intermolecular interactions are established to form a higher-order irreversible assembly, usually as result of aberrant liquid-liquid phase separation.") +AnnotationAssertion(Annotation( "PMID:33510441") "A higher-order assembly transition involving a non-native state of a protein in which insoluble intermolecular interactions are established to form a higher-order irreversible assembly, usually as result of aberrant liquid-liquid phase separation.") AnnotationAssertion( ) AnnotationAssertion( "PMID:38825008") AnnotationAssertion( "aggregate assembly") AnnotationAssertion( "aggregate formation") AnnotationAssertion( "protein aggregation") -AnnotationAssertion( "transition") +AnnotationAssertion( "higher-order assembly transition") AnnotationAssertion( "IDPO:0000066") AnnotationAssertion(rdfs:label "protein aggregate formation") SubClassOf( ) # Class: (amorphous aggregate formation) -AnnotationAssertion(Annotation( "PMID:40324497") "A process leading to the formation of a protein aggregate lacking stable or ordered structure.") +AnnotationAssertion(Annotation( "PMID:40324497") "A protein aggregate formation leading to the formation of a protein aggregate lacking stable or ordered structure.") AnnotationAssertion( ) AnnotationAssertion( "PMID:26735904") -AnnotationAssertion( "transition") +AnnotationAssertion( "higher-order assembly transition") AnnotationAssertion( "IDPO:0000067") AnnotationAssertion(rdfs:label "amorphous aggregate formation") SubClassOf( ) @@ -779,8 +780,8 @@ SubClassOf( (condensate material state) 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( "material state") +AnnotationAssertion( "physical state") AnnotationAssertion( "condensate material state") AnnotationAssertion( "IDPO:0000075") AnnotationAssertion(rdfs:label "condensate material state") @@ -826,26 +827,26 @@ AnnotationAssertion( "solid-like condensate state") SubClassOf( ) -# Class: (transition) +# Class: (DEPRECATED transition) -AnnotationAssertion( "A temporally extended process in which a protein or protein region changes from one state to another, under specific conditions.") -AnnotationAssertion( "transition") -AnnotationAssertion( "IDPO:0000080") -AnnotationAssertion(rdfs:label "transition") -SubClassOf( ) +AnnotationAssertion(rdfs:comment "Obsolete due to semantic ambiguity and excessive generality.") +AnnotationAssertion(rdfs:label "DEPRECATED transition") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Class: (transition to a more ordered state) -AnnotationAssertion( "A process in which a protein or protein region gains secondary and/or tertiary structure, leading to a more compacted or ordered conformation.") -AnnotationAssertion( "transition") +AnnotationAssertion( "A protein structural transition in which a protein or protein region gains secondary and/or tertiary structure, leading to a more compacted or ordered conformation.") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000081") AnnotationAssertion(rdfs:label "transition to a more ordered state") SubClassOf( ) # Class: (transition to a more disordered state) -AnnotationAssertion( "A process in which a protein or protein region losses secondary and/or tertiary structure, leading to a more extended or disordered conformation.") -AnnotationAssertion( "transition") +AnnotationAssertion( "A protein structural transition in which a protein or protein region loses secondary and/or tertiary structure, leading to a more extended or disordered conformation.") +AnnotationAssertion( "protein structural transition") AnnotationAssertion( "IDPO:0000082") AnnotationAssertion(rdfs:label "transition to a more disordered state") SubClassOf( ) @@ -853,16 +854,16 @@ SubClassOf( (higher-order assembly transition) AnnotationAssertion(Annotation( "PMID:33510441") "A biophysical process in which a biomolecular condensate or aggregate is formed or undergoes a change in material state.") -AnnotationAssertion( "transition") +AnnotationAssertion( "higher-order assembly transition") AnnotationAssertion( "IDPO:0000083") AnnotationAssertion(rdfs:label "higher-order assembly transition") -SubClassOf( ) +SubClassOf( ) # Class: (biomolecular condensate formation) -AnnotationAssertion( "A membraneless assembly process that concentrates specific biomolecules through weak, multivalent interactions. It may exhibit a well-mixed or spatially organized internal structure and can dynamically transition between different material states.") +AnnotationAssertion( "A higher-order assembly transition that concentrates specific biomolecules through weak, multivalent interactions. It may exhibit a well-mixed or spatially organized internal structure and can dynamically transition between different material states.") AnnotationAssertion( "biological condensate assembly") -AnnotationAssertion( "transition") +AnnotationAssertion( "higher-order assembly transition") AnnotationAssertion( "membraneless organelle assembly") AnnotationAssertion( "non-membrane-bounded organelle assembly") AnnotationAssertion( "IDPO:0000084")