diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 2fd28c3..aeaba3b 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -11,6 +11,7 @@ Import() Annotation( ) Annotation( ) Annotation( ) +Annotation( ) Annotation( "It describes structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state.") Annotation( ) Annotation( "Intrinsically Disordered Proteins Ontology") @@ -98,6 +99,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -454,305 +457,326 @@ AnnotationAssertion( "IDPO:0000029") AnnotationAssertion(rdfs:label "disorder function") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) -# Class: (entropic chain) +# Class: (entropic chain function) -AnnotationAssertion(Annotation( "PMID:12022860") "An intrinsically disordered region that enables a mechanical or regulatory function through its dynamic conformational flexibility, without adopting a stable tertiary structure.") +AnnotationAssertion(Annotation( "PMID:12022860") "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.") +AnnotationAssertion( "entropic chain") AnnotationAssertion( "entropic bristle") AnnotationAssertion( "entropic clock") AnnotationAssertion( "entropic spring") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000030") -AnnotationAssertion(rdfs:label "entropic chain") +AnnotationAssertion(rdfs:label "entropic chain function") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) -# Class: (flexible C-terminal tail) +# Class: (entropic chain function inhering in flexible C-terminal tail) -AnnotationAssertion( "An intrinsically disordered region located at the C-terminal end of a protein that enables regulatory or interaction-based functions through its conformational flexibility.") +AnnotationAssertion( "An entropic chain function that inheres in a flexible C-terminal tail of a protein.") AnnotationAssertion( "disordered terminal region") AnnotationAssertion( "C-terminal flexible tail") AnnotationAssertion( "disordered C-terminal tail") +AnnotationAssertion( "flexible C-terminal tail") AnnotationAssertion( "flexible C-terminus") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000031") -AnnotationAssertion(rdfs:label "flexible C-terminal tail") +AnnotationAssertion(rdfs:label "entropic chain function inhering in flexible C-terminal tail") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (flexible N-terminal tail) +# Class: (entropic chain function inhering in flexible N-terminal tail) -AnnotationAssertion( "An intrinsically disordered region located at the N-terminal end of a protein that enables regulatory or interaction-based functions through its conformational flexibility.") +AnnotationAssertion( "An entropic chain function that inheres in a flexible N-terminal tail of a protein.") AnnotationAssertion( "disordered terminal region") AnnotationAssertion( "N-terminal flexible tail") AnnotationAssertion( "disordered N-terminal tail") +AnnotationAssertion( "flexible N-terminal tail") AnnotationAssertion( "flexible N-terminus") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000032") -AnnotationAssertion(rdfs:label "flexible N-terminal tail") +AnnotationAssertion(rdfs:label "entropic chain function inhering in flexible N-terminal tail") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (flexible linker) +# Class: (entropic chain function inhering in flexible linker) -AnnotationAssertion(Annotation( "PMID:12022860") "An intrinsically disordered region that connects adjacent functional elements of a protein, providing spatial separation that permits independent yet coordinated activity.") +AnnotationAssertion(Annotation( "PMID:12022860") "An entropic chain function that inheres in a intrinsically disordered region comprising a flexible linker that connects adjacent functional elements of a protein, providing spatial separation that permits independent yet coordinated activity.") AnnotationAssertion( "disordered linker") +AnnotationAssertion( "flexible linker") AnnotationAssertion( "flexible spacer") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000033") -AnnotationAssertion(rdfs:label "flexible linker") +AnnotationAssertion(rdfs:label "entropic chain function inhering in flexible linker") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (short linear motif) +# Class: (short linear motif role) -AnnotationAssertion(Annotation( "PMID:25038412") "A transient molecular recognition interaction that is mediated by a short interaction interfaces enriched in an intrinsically disordered protein region.") +AnnotationAssertion(Annotation( "PMID:25038412") "A role in molecular recognition that inheres in a short intrinsically disordered protein region in virtue of its sequence complementarity to a specific binding partner, and is realized in a transient interaction with that partner.") AnnotationAssertion( ) -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000036") -AnnotationAssertion(rdfs:label "short linear motif") +AnnotationAssertion(rdfs:label "short linear motif role") SubClassOf( ) -# Class: (display site) +# Class: (post-translational modification target role) -AnnotationAssertion( "A protein region or residue that facilitates site-specific molecular recognition, serving as a platform for post-translational modifications.") +AnnotationAssertion( "A role in molecular recognition that inheres in a protein region in virtue of its recognition by a modifying enzyme or machinery, and is realized in the site-specific post-translational modification of that region.") +AnnotationAssertion( "display site") AnnotationAssertion( "post-translational modification site") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000037") -AnnotationAssertion(rdfs:label "display site") +AnnotationAssertion(rdfs:label "post-translational modification target role") SubClassOf( ) -# Class: (ADP-ribosylation display site) +# Class: (ADP-ribosylation target role) -AnnotationAssertion( "A molecular recognition site that serves as the target for the addition of one or more ADP-ribose moietyes.") +AnnotationAssertion( "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by an ADP-ribosyltransferase, and is realized in the addition of one or more ADP-ribose moieties to that region.") +AnnotationAssertion( "ADP-ribosylation display site") AnnotationAssertion( "mono-ADP ribosylation site") AnnotationAssertion( "poly-ADP ribosylation site") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000038") -AnnotationAssertion(rdfs:label "ADP-ribosylation display site") +AnnotationAssertion(rdfs:label "ADP-ribosylation target role") SubClassOf( ) -# Class: (acetylation display site) +# Class: (acetylation target role) -AnnotationAssertion( "A molecular recognition site that serves as the target for the covalent attachment of an acetyl group.") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by an acetyltransferase, and is realized in the covalent attachment of an acetyl group to that region.") +AnnotationAssertion( "acetylation display site") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000039") -AnnotationAssertion(rdfs:label "acetylation display site") +AnnotationAssertion(rdfs:label "acetylation target role") SubClassOf( ) -# Class: (fatty acylation display site) +# Class: (fatty acylation target role) -AnnotationAssertion( "A molecular recognition site that serves as the target for the addition of fatty acyl groups.") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by a fatty acyltransferase, and is realized in the covalent addition of a fatty acyl group to that region.") +AnnotationAssertion( "fatty acylation display site") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000040") -AnnotationAssertion(rdfs:label "fatty acylation display site") +AnnotationAssertion(rdfs:label "fatty acylation target role") SubClassOf( ) -# Class: (glycosylation display site) +# Class: (glycosylation target role) -AnnotationAssertion( "A molecular recognition site that serves as the target for the covalent addition of a sugar.") +AnnotationAssertion( "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.") +AnnotationAssertion( "glycosylation display site") AnnotationAssertion( "N-linked glycosylation site") AnnotationAssertion( "O-linked glycosylation site") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000041") -AnnotationAssertion(rdfs:label "glycosylation display site") +AnnotationAssertion(rdfs:label "glycosylation target role") SubClassOf( ) -# Class: (methylation display site) +# Class: (methylation target role) -AnnotationAssertion( "A molecular recognition site that serves as the target for the covalent addition of a methyl groups.") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by a methyltransferase, and is realized in the covalent addition of a methyl group to that region.") +AnnotationAssertion( "methylation display site") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000042") -AnnotationAssertion(rdfs:label "methylation display site") +AnnotationAssertion(rdfs:label "methylation target role") SubClassOf( ) -# Class: (myristoylation display site) +# Class: (myristoylation target role) -AnnotationAssertion( "A molecular recognition site that serves as the target for the co-translational or post-translational attachment of a myristoyl group.") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by an N-myristoyltransferase, and is realized in the co-translational or post-translational attachment of a myristoyl group to that region.") +AnnotationAssertion( "myristoylation display site") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000043") -AnnotationAssertion(rdfs:label "myristoylation display site") +AnnotationAssertion(rdfs:label "myristoylation target role") SubClassOf( ) -# Class: (palmitoylation display site) +# Class: (palmitoylation target role) -AnnotationAssertion( "A molecular recognition site that serves as the target for the reversible attachment of a palmitoyl groups.") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by a palmitoyltransferase, and is realized in the reversible attachment of a palmitoyl group to that region.") +AnnotationAssertion( "palmitoylation display site") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000044") -AnnotationAssertion(rdfs:label "palmitoylation display site") +AnnotationAssertion(rdfs:label "palmitoylation target role") SubClassOf( ) -# Class: (phosphorylation display site) +# Class: (phosphorylation target role) -AnnotationAssertion( "A molecular recognition site that serves as the target for the covalent addition of a phosphate group.") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by a protein kinase, and is realized in the covalent addition of a phosphate group to that region.") +AnnotationAssertion( "phosphorylation display site") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000045") -AnnotationAssertion(rdfs:label "phosphorylation display site") +AnnotationAssertion(rdfs:label "phosphorylation target role") SubClassOf( ) -# Class: (ubiquitination display site) +# Class: (ubiquitination target role) -AnnotationAssertion( "A molecular recognition site that serves as the target for the covalent attachment of a ubiquitin moeity.") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by a ubiquitin ligase, and is realized in the covalent attachment of a ubiquitin moiety to that region.") +AnnotationAssertion( "ubiquitination display site") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000046") -AnnotationAssertion(rdfs:label "ubiquitination display site") +AnnotationAssertion(rdfs:label "ubiquitination target role") SubClassOf( ) -# Class: (cleavage motif) +# Class: (cleavage motif role) -AnnotationAssertion(Annotation( "PMID:19920119") "A short linear motif that serves as the recognition site for proteolytic enzymes.") +AnnotationAssertion(Annotation( "PMID:19920119") "A short linear motif role that inheres in a protein region in virtue of its recognition by a proteolytic enzyme, and is realized in the cleavage of the polypeptide chain at that region.") AnnotationAssertion( ) -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000047") -AnnotationAssertion(rdfs:label "cleavage motif") +AnnotationAssertion(rdfs:label "cleavage motif role") SubClassOf( ) -# Class: (limited proteolysis display site) +# Class: (limited proteolysis target role) -AnnotationAssertion( "A molecular recognition site that serves as the target of the cleavage of the polypeptide chain.") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "A role in molecular recognition that inheres in an intrinsically disordered protein region in virtue of its recognition by a protease, and is realized in the regulatory cleavage of the polypeptide chain at that region.") +AnnotationAssertion( "limited proteolysis display site") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000048") -AnnotationAssertion(rdfs:label "limited proteolysis display site") -SubClassOf( ) +AnnotationAssertion(rdfs:label "limited proteolysis target role") +SubClassOf( ) -# Class: (degron motif) +# Class: (degron motif role) -AnnotationAssertion(Annotation( "PMID:24214962") "A short linear motif that directs protein polyubiquitylation and targets the protein to the proteasome for degradation.") +AnnotationAssertion(Annotation( "PMID:24214962") "A short linear motif role that inheres in a protein region in virtue of its recognition by a ubiquitin ligase complex, and is realized in the direction of protein polyubiquitylation and targeting to the proteasome for degradation.") AnnotationAssertion( ) AnnotationAssertion( "PMID:12820959") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000049") -AnnotationAssertion(rdfs:label "degron motif") +AnnotationAssertion(rdfs:label "degron motif role") SubClassOf( ) -# Class: (docking motif) +# Class: (docking motif role) -AnnotationAssertion(Annotation( "PMID:24214962") "A short linear motif that recruits a modifying enzyme using a site that is distinct from the active site.") +AnnotationAssertion(Annotation( "PMID:24214962") "A short linear motif role that inheres in a protein region in virtue of its recognition by a modifying enzyme at an allosteric or regulatory site distinct from the enzyme's active site, and is realized in the recruitment of that enzyme to the substrate.") AnnotationAssertion( ) AnnotationAssertion( "PMID:8684460") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000050") -AnnotationAssertion(rdfs:label "docking motif") +AnnotationAssertion(rdfs:label "docking motif role") SubClassOf( ) -# Class: (ligand binding motif) +# Class: (ligand binding motif role) -AnnotationAssertion(Annotation( "PMID:21909575") "A short linear motif that mediate binding of the ligand protein to its interaction partner.") +AnnotationAssertion(Annotation( "PMID:21909575") "A short linear motif role that inheres in a protein region in virtue of its sequence complementarity to a specific interaction partner, and is realized in the binding of the protein to that partner.") AnnotationAssertion( ) AnnotationAssertion( "PMID:26888287") -AnnotationAssertion( "ligand-binding motif") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000051") -AnnotationAssertion(rdfs:label "ligand binding motif") +AnnotationAssertion(rdfs:label "ligand binding motif role") SubClassOf( ) -# Class: (targeting motif) +# Class: (targeting motif role) -AnnotationAssertion(Annotation( "PMID:19920119") "A short linear motif that mediates recognition and targeting to subcellular compartments.") +AnnotationAssertion(Annotation( "PMID:19920119") "A short linear motif role that inheres in a protein region in virtue of its recognition by subcellular targeting machinery, and is realized in the targeting of the protein to a specific subcellular compartment.") AnnotationAssertion( ) AnnotationAssertion( "PMID:12417334") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000052") -AnnotationAssertion(rdfs:label "targeting motif") +AnnotationAssertion(rdfs:label "targeting motif role") SubClassOf( ) -# Class: (self interaction) +# Class: (intramolecular interaction function) -AnnotationAssertion( "Protein intramolecular interaction where one region of the protein engages with another region within the same protein, affecting its assembly or function.") +AnnotationAssertion( "A disorder function that inheres in a protein region in virtue of its structural complementarity to another region of the same protein, and is realized in an intramolecular interaction that affects the protein's conformation, assembly, or activity.") +AnnotationAssertion( "self interaction") AnnotationAssertion( "self-interaction") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000056") -AnnotationAssertion(rdfs:label "self interaction") -SubClassOf( ) +AnnotationAssertion(rdfs:label "intramolecular interaction function") +SubClassOf( ) -# Class: (self regulatory activity) +# Class: (autoregulatory function) -AnnotationAssertion( "An intramolecular mechanism by which a protein modulates its own activity.") +AnnotationAssertion( "An intramolecular interaction function that inheres in a protein region and is realized in the modulation of the protein's own activity through intramolecular contact.") AnnotationAssertion( "autoregulatory activity") +AnnotationAssertion( "self regulatory activity") AnnotationAssertion( "self-regulatory activity") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000057") -AnnotationAssertion(rdfs:label "self regulatory activity") +AnnotationAssertion(rdfs:label "autoregulatory function") SubClassOf( ) -# Class: (self activation) +# Class: (autoactivation function) -AnnotationAssertion( "A self regulatory mechanism in which intramolecular interactions induce or enhance the functional activity of a protein.") +AnnotationAssertion( "An autoregulatory function that inheres in a protein region and is realized in the induction or enhancement of the protein's own activity through intramolecular contact.") AnnotationAssertion( "autoactivation") +AnnotationAssertion( "self activation") AnnotationAssertion( "self-activation") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000058") -AnnotationAssertion(rdfs:label "self activation") +AnnotationAssertion(rdfs:label "autoactivation function") SubClassOf( ) -# Class: (self inhibition) +# Class: (autoinhibition function) -AnnotationAssertion( "A self regulatory mechanism in which intramolecular interactions repress or prevent the functional activity of a protein.") +AnnotationAssertion( "An autoregulatory function that inheres in a protein region and is realized in the suppression or prevention of the protein's own activity through intramolecular contact.") AnnotationAssertion( "autoinhibition") +AnnotationAssertion( "self inhibition") AnnotationAssertion( "self-inhibition") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000059") -AnnotationAssertion(rdfs:label "self inhibition") +AnnotationAssertion(rdfs:label "autoinhibition function") SubClassOf( ) -# Class: (self assembly) +# Class: (intramolecular assembly function) -AnnotationAssertion( "A process by which distinct regions within a single protein interact to promote its conformational organization into higher-order structures.") +AnnotationAssertion( "An intramolecular interaction function that inheres in a protein region and is realized in its association with one or more other regions of the same protein to promote a specific conformational organisation of the protein.") +AnnotationAssertion( "self assembly") AnnotationAssertion( "self-assembly") AnnotationAssertion( "disorder_function") AnnotationAssertion( "IDPO:0000060") -AnnotationAssertion(rdfs:label "self assembly") +AnnotationAssertion(rdfs:label "intramolecular assembly function") SubClassOf( ) -# Class: (functional role in condensate assembly) +# Class: (role in condensate assembly) -AnnotationAssertion( "A protein or protein region that promotes or participates in the formation of a biomolecular condensate.") +AnnotationAssertion( "A disorder role that inheres in a protein or protein region in virtue of its physicochemical properties that promote or enable participation in condensate formation, and is realized in the formation of or participation in a biomolecular condensate.") AnnotationAssertion( ) AnnotationAssertion( "biomolecular condensate assembler") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000061") -AnnotationAssertion(rdfs:label "functional role in condensate assembly") -SubClassOf( ) +AnnotationAssertion(rdfs:label "role in condensate assembly") +SubClassOf( ) -# Class: (driver) +# Class: (driver role in condensate assembly) -AnnotationAssertion(Annotation( "PMID:33809541") "A protein or protein region with high interaction valence necessary and sufficient for liquid-liquid phase separation.") +AnnotationAssertion(Annotation( "PMID:33809541") "A role in condensate assembly that inheres in a protein or protein region in virtue of its high interaction valence, and is realized in the nucleation and maintenance of liquid-liquid phase separation.") AnnotationAssertion( ) +AnnotationAssertion( "driver") AnnotationAssertion( "scaffold") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000062") -AnnotationAssertion(rdfs:label "driver") +AnnotationAssertion(rdfs:label "driver role in condensate assembly") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -# Class: (co-driver) +# Class: (co-driver role in condensate assembly) -AnnotationAssertion(Annotation( "PMID:33809541") "A protein or protein region that strictly requires one or more partners to enable liquid–liquid phase separation, and unlike regulators, physically incorporates into the scaffold of the resulting condensate.") +AnnotationAssertion(Annotation( "PMID:33809541") "A role in condensate assembly that inheres in a protein or protein region in virtue of its capacity to promote liquid-liquid phase separation strictly in the presence of one or more partner molecules, and is realized in phase separation with physical incorporation of the bearer into the condensate scaffold.") AnnotationAssertion( ) -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "co-driver") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000063") -AnnotationAssertion(rdfs:label "co-driver") +AnnotationAssertion(rdfs:label "co-driver role in condensate assembly") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulator) +# Class: (regulator role in condensate assembly) -AnnotationAssertion(Annotation( "PMID:33809541") "A protein or protein region that facilitates or modulates the liquid–liquid phase separation of one or more driver or co-driver molecules without being physically incorporated into the resulting condensate.") +AnnotationAssertion(Annotation( "PMID:33809541") "A role in condensate assembly that inheres in a protein or protein region in virtue of its capacity to modulate the phase separation of driver or co-driver molecules, and is realized in the facilitation or inhibition of liquid-liquid phase separation without physical incorporation of the bearer into the condensate.") AnnotationAssertion( ) -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "regulator") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000064") -AnnotationAssertion(rdfs:label "regulator") +AnnotationAssertion(rdfs:label "regulator role in condensate assembly") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -# Class: (client) +# Class: (client role in condensate assembly) -AnnotationAssertion(Annotation( "PMID:33809541") "A protein or protein region with lower valence recruited into condensates formed by scaffolds, but it is not required for and does not have an effect on liquid-liquid phase separation.") +AnnotationAssertion(Annotation( "PMID:33809541") "A role in condensate assembly that inheres in a protein or protein region in virtue of its low interaction valence, and is realized in its recruitment into a condensate formed by scaffold molecules without contributing to or affecting the phase separation process itself.") AnnotationAssertion( ) -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000065") -AnnotationAssertion(rdfs:label "client") +AnnotationAssertion(rdfs:label "client role in condensate assembly") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (protein aggregate formation) @@ -870,23 +894,24 @@ AnnotationAssertion( "biomolecular condensate formation") SubClassOf( ) -# Class: (molecular recognition) +# Class: (role in molecular recognition) -AnnotationAssertion( "A functional capability of a molecule or molecular region to selectively interact with a partner or itself, recognition may be transient or stable and may be mediated by domains, short linear motifs, or disordered regions.") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "A disorder role that inheres in an intrinsically disordered protein region in virtue of its sequence or structural properties being recognised by a molecular partner, and is realized in a molecular recognition process.") +AnnotationAssertion( "molecular recognition") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000085") -AnnotationAssertion(rdfs:label "molecular recognition") -SubClassOf( ) +AnnotationAssertion(rdfs:label "role in molecular recognition") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) -# Class: (post-translational modification motif) +# Class: (post-translational modification motif role) -AnnotationAssertion(Annotation( "PMID:25038412") "A short linear motif that directs site-specific post-translational modification.") +AnnotationAssertion(Annotation( "PMID:25038412") "A short linear motif role that inheres in a protein region in virtue of its recognition by a PTM enzyme, and is realized in the direction of site-specific post-translational modification of the protein, either at that region or at a proximal site.") AnnotationAssertion( ) AnnotationAssertion( "PMID:11463845") -AnnotationAssertion( "PTM motif") -AnnotationAssertion( "disorder_function") +AnnotationAssertion( "disorder_role") AnnotationAssertion( "IDPO:0000086") -AnnotationAssertion(rdfs:label "post-translational modification motif") +AnnotationAssertion(rdfs:label "post-translational modification motif role") SubClassOf( ) # Class: (DEPRECATED state) @@ -953,6 +978,24 @@ AnnotationAssertion( "ordered region") SubClassOf( ) +# Class: (SUMOylation target role) + +AnnotationAssertion( "A post-translational modification target role that inheres in an intrinsically disordered protein region in virtue of its recognition by a SUMO E3 ligase, and is realized in the covalent attachment of a small ubiquitin-like modifier (SUMO) protein to that region.") +AnnotationAssertion( "SUMOylation display site") +AnnotationAssertion( "disorder_role") +AnnotationAssertion( "IDPO:0000099") +AnnotationAssertion(rdfs:label "SUMOylation target role") +SubClassOf( ) + +# Class: (disorder role) + +AnnotationAssertion( "A role that inheres in an intrinsically disordered protein or protein region in virtue of its conformational flexibility within a biological context, and is realized in a process that depends on that flexibility.") +AnnotationAssertion( "disorder_role") +AnnotationAssertion( "IDPO:0000100") +AnnotationAssertion(rdfs:label "disorder role") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) )