diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 1b8a81e..e64e31c 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -114,6 +114,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:label)) ############################ @@ -417,18 +418,16 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (liquid liquid phase separation) +# Class: (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( ) "LLPS") - AnnotationAssertion( ) AnnotationAssertion( "PMID:38287572") +AnnotationAssertion(Annotation( ) "LLPS") AnnotationAssertion( "liquid–liquid demixing") -AnnotationAssertion( "liquid-liquid phase separation") AnnotationAssertion( "transition") AnnotationAssertion( "IDPO:0000025") -AnnotationAssertion(rdfs:label "liquid liquid phase separation") +AnnotationAssertion(rdfs:label "liquid-liquid phase separation") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -452,6 +451,7 @@ AnnotationAssertion(Annotation( "PMI AnnotationAssertion( ) AnnotationAssertion( "PMID:22579281") AnnotationAssertion( "liquid to gel transition") +AnnotationAssertion( "condensate gelation") AnnotationAssertion( "transition") AnnotationAssertion( "IDPO:0000027") AnnotationAssertion(rdfs:label "gelation") @@ -464,6 +464,7 @@ SubClassOf( ObjectSomeValuesFrom( "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( ) AnnotationAssertion( "liquid to glass transition") +AnnotationAssertion( "condensate crystallization") AnnotationAssertion( "transition") AnnotationAssertion( "IDPO:0000028") AnnotationAssertion(rdfs:label "crystallization") @@ -664,6 +665,7 @@ SubClassOf( "PMID:21909575") "A short linear motif that mediate binding of the ligand protein to its interaction partner.") AnnotationAssertion( ) AnnotationAssertion( "PMID:26888287") +AnnotationAssertion( "ligand-binding motif") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000051") AnnotationAssertion(rdfs:label "ligand binding motif") @@ -682,6 +684,7 @@ SubClassOf( (self interaction) AnnotationAssertion( "Protein intramolecular interaction where one region of the protein engages with another region within the same protein, affecting its assembly or function.") +AnnotationAssertion( "self-interaction") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000056") AnnotationAssertion(rdfs:label "self interaction") @@ -691,6 +694,7 @@ SubClassOf( "An intramolecular mechanism by which a protein modulates its own activity.") AnnotationAssertion( "autoregulatory activity") +AnnotationAssertion( "self-regulatory activity") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000057") AnnotationAssertion(rdfs:label "self regulatory activity") @@ -700,6 +704,7 @@ SubClassOf( "A self-regulatory mechanism in which intramolecular interactions induce or enhance the functional activity of a protein.") AnnotationAssertion( "autoactivation") +AnnotationAssertion( "self-activation") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000058") AnnotationAssertion(rdfs:label "self activation") @@ -709,6 +714,7 @@ SubClassOf( "A self-regulatory mechanism in which intramolecular interactions repress or prevent the functional activity of a protein.") AnnotationAssertion( "autoinhibition") +AnnotationAssertion( "self-inhibition") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000059") AnnotationAssertion(rdfs:label "self inhibition") @@ -717,6 +723,7 @@ SubClassOf( (self assembly) AnnotationAssertion( "A process by which distinct regions within a single protein interact to promote its conformational organization into higher-order structures.") +AnnotationAssertion( "self-assembly") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000060") AnnotationAssertion(rdfs:label "self assembly") @@ -779,6 +786,8 @@ AnnotationAssertion(Annotation( "PMI AnnotationAssertion( ) AnnotationAssertion( "PMID:38825008") AnnotationAssertion( "aggregate formation") +AnnotationAssertion( "aggregate assembly") +AnnotationAssertion( "protein aggregation") AnnotationAssertion( "transition") AnnotationAssertion( "IDPO:0000066") AnnotationAssertion(rdfs:label "protein aggregate formation") @@ -803,43 +812,43 @@ AnnotationAssertion( "material state") SubClassOf( ) -# Class: (liquid like state) +# Class: (liquid-like 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( "PMID:38287572") AnnotationAssertion( "state") AnnotationAssertion( "liquid-like condensate") AnnotationAssertion( "IDPO:0000076") -AnnotationAssertion(rdfs:label "liquid like state") +AnnotationAssertion(rdfs:label "liquid-like state") SubClassOf( ) -# Class: (gel like state) +# Class: (gel-like 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( "PMID:34102212") AnnotationAssertion( "state") AnnotationAssertion( "gel-like condensate") AnnotationAssertion( "IDPO:0000077") -AnnotationAssertion(rdfs:label "gel like state") +AnnotationAssertion(rdfs:label "gel-like state") SubClassOf( ) -# Class: (glass like state) +# Class: (glass-like 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( "glass-like condensate") AnnotationAssertion( "IDPO:0000078") -AnnotationAssertion(rdfs:label "glass like state") +AnnotationAssertion(rdfs:label "glass-like state") SubClassOf( ) -# Class: (solid like state) +# Class: (solid-like 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( "PMID:34095780") AnnotationAssertion( "state") AnnotationAssertion( "solid-like condensate") AnnotationAssertion( "IDPO:0000079") -AnnotationAssertion(rdfs:label "solid like state") +AnnotationAssertion(rdfs:label "solid-like state") SubClassOf( ) # Class: (transition) @@ -867,13 +876,12 @@ AnnotationAssertion( "transition to a more disordered state") SubClassOf( ) -# Class: (higher order assembly transition) +# Class: (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( "higher-order assembly transition") AnnotationAssertion( "transition") AnnotationAssertion( "IDPO:0000083") -AnnotationAssertion(rdfs:label "higher order assembly transition") +AnnotationAssertion(rdfs:label "higher-order assembly transition") SubClassOf( ) # Class: (biomolecular condensate formation)