From a420d37e9156c1ae195e49ac9f484494c35131b3 Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Thu, 1 Aug 2024 13:25:14 +0100 Subject: [PATCH 1/2] Update cl-edit.owl --- src/ontology/cl-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 0bcdffd1d..cab65df9d 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -5463,14 +5463,14 @@ SubClassOf(obo:CL_0000209 obo:CL_0002076) # Class: obo:CL_0000210 (photoreceptor cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D010786") obo:IAO_0000115 obo:CL_0000210 "A cell specialized to detect and transduce light.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D010786") obo:IAO_0000115 obo:CL_0000210 "A cell specialized in detecting light stimuli that are involved in visual perception.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000210 "BTO:0001060") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000210 "CALOHA:TS-0868") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000210 "FMA:86740") AnnotationAssertion(rdfs:label obo:CL_0000210 "photoreceptor cell") AnnotationAssertion(foaf:depiction obo:CL_0000210 "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg"^^xsd:anyURI) -EquivalentClasses(obo:CL_0000210 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050962))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000210 obo:CL_0000006) +EquivalentClasses(obo:CL_0000210 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050908))) +SubClassOf(obo:CL_0000210 obo:CL_0008028) # Class: obo:CL_0000211 (electrically active cell) From 1f3b19593973fa05552089a5c0226e9f8a6bc3c1 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 19 Sep 2024 12:19:45 +0100 Subject: [PATCH 2/2] Update imports --- src/ontology/imports/merged_import.owl | 625 +++++++++++-------------- src/patterns/definitions.owl | 4 +- 2 files changed, 275 insertions(+), 354 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 77e2a5c2e..9ecc18343 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-09-13") + +Annotation(owl:versionInfo "2024-09-19") Declaration(Class()) Declaration(Class()) @@ -93,7 +93,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1496,7 +1495,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1995,7 +1993,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2299,7 +2296,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3148,12 +3144,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4934,6 +4928,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5607,7 +5602,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5749,7 +5743,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5801,7 +5794,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6794,9 +6786,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6912,7 +6901,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7030,7 +7018,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7273,7 +7260,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8254,6 +8240,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -14160,6 +14147,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14465,6 +14453,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -17306,6 +17298,7 @@ SubClassOf( (chromatin) AnnotationAssertion(Annotation( "GOC:elh") Annotation( "PMID:20404130") "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28301"^^xsd:anyURI) AnnotationAssertion( "GO:0000789") AnnotationAssertion( "GO:0000790") AnnotationAssertion( "GO:0005717") @@ -17317,7 +17310,7 @@ AnnotationAssertion( "GO:0000785") AnnotationAssertion(rdfs:comment "Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.") AnnotationAssertion(rdfs:label "chromatin") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (euchromatin) @@ -19204,15 +19197,18 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein phosphorylation) AnnotationAssertion(Annotation( "GOC:hjd") "Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28278"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:bf") "regulation of protein amino acid phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0001932") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of protein phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (negative regulation of protein phosphorylation) AnnotationAssertion(Annotation( "GOC:hjd") "Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28278"^^xsd:anyURI) AnnotationAssertion( "down regulation of protein amino acid phosphorylation") AnnotationAssertion( "down-regulation of protein amino acid phosphorylation") AnnotationAssertion( "downregulation of protein amino acid phosphorylation") @@ -19220,6 +19216,7 @@ AnnotationAssertion(Annotation( "inhibition of protein amino acid phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0001933") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of protein phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -19227,6 +19224,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:hjd") "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28278"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:bf") "positive regulation of protein amino acid phosphorylation") AnnotationAssertion( "up regulation of protein amino acid phosphorylation") AnnotationAssertion( "up-regulation of protein amino acid phosphorylation") @@ -19235,7 +19233,7 @@ AnnotationAssertion( "stimulation of protein amino acid phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0001934") -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of protein phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -19488,7 +19486,7 @@ AnnotationAssertion( "renal blood volume control of blood pressure") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "renal regulation of blood volume") AnnotationAssertion( "GO:0001977") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal system process involved in regulation of blood volume") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21904,15 +21902,17 @@ AnnotationAssertion( "nitric oxide production involved in inflammatory response") SubClassOf( ) -# Class: (arachidonic acid metabolite production involved in inflammatory response) +# Class: (arachidonate metabolite production involved in inflammatory response) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") "The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28648"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:mah") "arachidonic acid metabolite production involved in acute inflammatory response") AnnotationAssertion( "production of arachidonic acid metabolites involved in acute inflammatory response") +AnnotationAssertion( "arachidonic acid metabolite production involved in inflammatory response") AnnotationAssertion( "production of arachidonic acid metabolites involved in inflammatory response") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002538") -AnnotationAssertion(rdfs:label "arachidonic acid metabolite production involved in inflammatory response") +AnnotationAssertion(rdfs:label "arachidonate metabolite production involved in inflammatory response") SubClassOf( ) # Class: (prostaglandin production involved in inflammatory response) @@ -26826,7 +26826,8 @@ SubClassOf( "RHEA:10596") "Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.") AnnotationAssertion( "GO:0004718") -AnnotationAssertion(Annotation( "skos:narrowMatch") "EC:2.7.10.2") +AnnotationAssertion(Annotation( "skos:exactMatch") "EC:2.7.10.-") +AnnotationAssertion( "MetaCyc:2.7.10.1-RXN") AnnotationAssertion(Annotation( "skos:exactMatch") "RHEA:10596") AnnotationAssertion(Annotation(rdfs:label "SRC autophosphorylation is positively regulated by InlA-bound CDH1") "Reactome:R-HSA-112333") AnnotationAssertion(Annotation(rdfs:label "Fyn/Lyn-mediated phosphorylation of FcR1 gamma") "Reactome:R-HSA-114600") @@ -27218,8 +27219,8 @@ SubClassOf( ObjectSomeValuesFrom( (transmembrane receptor protein tyrosine kinase activity) AnnotationAssertion(Annotation( "EC:2.7.10.1") Annotation( "GOC:mah") "Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28176"^^xsd:anyURI) AnnotationAssertion(Annotation( "skos:exactMatch") "EC:2.7.10.1") -AnnotationAssertion( "MetaCyc:2.7.10.1-RXN") AnnotationAssertion(Annotation(rdfs:label "TrkA receptor autophosphorylates") "Reactome:R-HSA-166544") AnnotationAssertion(Annotation(rdfs:label "SHC, complexed with TrkA, is tyrosine-phosphorylated") "Reactome:R-HSA-167019") AnnotationAssertion(Annotation(rdfs:label "TrkA phosphorylates PLCG1") "Reactome:R-HSA-167683") @@ -27542,6 +27543,8 @@ SubClassOf( "ISBN:0198506732") "Combining with insulin receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23056"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28520"^^xsd:anyURI) +AnnotationAssertion(Annotation( "skos:broadMatch") "EC:2.7.10.1") AnnotationAssertion(Annotation(rdfs:label "Autophosphorylation of insulin receptor") "Reactome:R-HSA-74715") AnnotationAssertion( "insulin-activated receptor activity") AnnotationAssertion( "molecular_function") @@ -27873,7 +27876,7 @@ AnnotationAssertion( "GO:0005319") AnnotationAssertion(rdfs:label "lipid transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) # Class: (neurotransmitter transmembrane transporter activity) @@ -27884,7 +27887,7 @@ AnnotationAssertion( "neurotransmitter transporter activity") AnnotationAssertion( "GO:0005326") AnnotationAssertion(rdfs:label "neurotransmitter transmembrane transporter activity") -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) @@ -27908,21 +27911,6 @@ AnnotationAssertion(rdfs:label "ATP EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (glucose transmembrane transporter activity) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:mtg_transport") Annotation( "ISBN:0815340729") "Enables the transfer of the hexose monosaccharide glucose from one side of a membrane to the other.") -AnnotationAssertion( "GO:0015579") -AnnotationAssertion(Annotation(rdfs:label "Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2") "Reactome:R-HSA-499981") -AnnotationAssertion(Annotation(rdfs:label "SLC2A1 tetramer transports Glc from cytosol to Golgi lumen") "Reactome:R-HSA-5653873") -AnnotationAssertion( "glucose permease activity") -AnnotationAssertion( "lactose/glucose efflux transporter activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "galactose/glucose (methylgalactoside) porter activity") -AnnotationAssertion( "GO:0005355") -AnnotationAssertion(rdfs:label "glucose transmembrane transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (water transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:ai") "Enables the transfer of water (H2O) from one side of a membrane to the other.") @@ -27968,7 +27956,6 @@ AnnotationAssertion( "GO:0005488") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.") AnnotationAssertion(rdfs:label "binding") SubClassOf( ) @@ -28927,9 +28914,10 @@ SubClassOf( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27107"^^xsd:anyURI) -AnnotationAssertion( "MetaCyc:GLYCOGENSYNTH-PWY") -AnnotationAssertion( "MetaCyc:PWY-5067") -AnnotationAssertion( "MetaCyc:PWY-7900") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28527"^^xsd:anyURI) +AnnotationAssertion(Annotation( "skos:narrowMatch") "MetaCyc:GLYCOGENSYNTH-PWY") +AnnotationAssertion(Annotation( "skos:narrowMatch") "MetaCyc:PWY-5067") +AnnotationAssertion(Annotation( "skos:narrowMatch") "MetaCyc:PWY-7900") AnnotationAssertion( "glycogen anabolism") AnnotationAssertion( "glycogen biosynthesis") AnnotationAssertion( "glycogen formation") @@ -28959,9 +28947,10 @@ SubClassOf( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27107"^^xsd:anyURI) -AnnotationAssertion( "MetaCyc:GLYCOCAT-PWY") -AnnotationAssertion( "MetaCyc:PWY-5941") -AnnotationAssertion( "MetaCyc:PWY-7662") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28527"^^xsd:anyURI) +AnnotationAssertion(Annotation( "skos:narrowMatch") "MetaCyc:GLYCOCAT-PWY") +AnnotationAssertion(Annotation( "skos:narrowMatch") "MetaCyc:PWY-5941") +AnnotationAssertion(Annotation( "skos:narrowMatch") "MetaCyc:PWY-7662") AnnotationAssertion( "glycogen breakdown") AnnotationAssertion( "glycogen catabolism") AnnotationAssertion( "glycogen degradation") @@ -29523,7 +29512,7 @@ AnnotationAssertion(Annotation( "GOC:bf") "protein amino acid phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006468") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein phosphorylation") SubClassOf( ) @@ -29538,7 +29527,7 @@ AnnotationAssertion( "inhibition of protein kinase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006469") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of protein kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -29740,7 +29729,6 @@ AnnotationAssertion( "cellular modified amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (biogenic amine metabolic process) @@ -30639,6 +30627,7 @@ SubClassOf( (response to stress) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26810"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "response to abiotic stress") AnnotationAssertion( "response to biotic stress") @@ -30649,7 +30638,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "response to stress") SubClassOf( ) @@ -31474,6 +31462,9 @@ SubClassOf( (gamete generation) AnnotationAssertion(Annotation( "GOC:ems") Annotation( "GOC:mtg_sensu") "The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "GO:0009552") AnnotationAssertion( "biological_process") AnnotationAssertion( "gametogenesis") @@ -31481,7 +31472,16 @@ AnnotationAssertion( "gamete generation") SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (pole cell development) @@ -32603,6 +32603,8 @@ AnnotationAssertion( "axo-dendritic transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (anterograde axonal transport) @@ -33077,7 +33079,7 @@ AnnotationAssertion( "GO:0008320") AnnotationAssertion(rdfs:label "protein transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) # Class: (monoatomic cation transmembrane transporter activity) @@ -33231,7 +33233,7 @@ AnnotationAssertion( "GO:0008519") AnnotationAssertion(rdfs:label "ammonium channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (G protein-coupled peptide receptor activity) @@ -34669,19 +34671,6 @@ AnnotationAssertion(rdfs:label "vasc SubClassOf( ) SubClassOf( ) -# Class: (response to organonitrogen compound) - -AnnotationAssertion(Annotation( "PMID:9869419") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) -AnnotationAssertion( "response to organic nitrogen") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010243") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "response to organonitrogen compound") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (endomembrane system organization) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:sm") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system.") @@ -34795,7 +34784,7 @@ AnnotationAssertion( "regulation of signalling receptor activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010469") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of signaling receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -35676,31 +35665,34 @@ AnnotationAssertion( "positive regulation of T cell chemotaxis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of glucose transmembrane transport) +# Class: (regulation of D-glucose transmembrane transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "regulation of glucose transmembrane transport") AnnotationAssertion( "biological_process") AnnotationAssertion( "regulation of glucose transport") AnnotationAssertion( "GO:0010827") -AnnotationAssertion(rdfs:label "regulation of glucose transmembrane transport") +AnnotationAssertion(rdfs:label "regulation of D-glucose transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (positive regulation of glucose transmembrane transport) +# Class: (positive regulation of D-glucose transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "positive regulation of glucose transmembrane transport") AnnotationAssertion( "biological_process") AnnotationAssertion( "positive regulation of glucose transport") AnnotationAssertion( "GO:0010828") -AnnotationAssertion(rdfs:label "positive regulation of glucose transmembrane transport") +AnnotationAssertion(rdfs:label "positive regulation of D-glucose transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (negative regulation of glucose transmembrane transport) +# Class: (negative regulation of D-glucose transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "negative regulation of glucose transmembrane transport") AnnotationAssertion( "biological_process") AnnotationAssertion( "negative regulation of glucose transport") AnnotationAssertion( "GO:0010829") -AnnotationAssertion(rdfs:label "negative regulation of glucose transmembrane transport") +AnnotationAssertion(rdfs:label "negative regulation of D-glucose transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (regulation of myotube differentiation) @@ -37237,7 +37229,7 @@ AnnotationAssertion( "GO:0015075") AnnotationAssertion(rdfs:label "monoatomic ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) # Class: (proton transmembrane transporter activity) @@ -37254,7 +37246,7 @@ AnnotationAssertion( "GO:0015078") AnnotationAssertion(rdfs:label "proton transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) # Class: (potassium ion transmembrane transporter activity) @@ -37269,7 +37261,7 @@ AnnotationAssertion( "GO:0015079") AnnotationAssertion(rdfs:label "potassium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sodium ion transmembrane transporter activity) @@ -37339,7 +37331,7 @@ AnnotationAssertion( "GO:0015144") AnnotationAssertion(rdfs:label "carbohydrate transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) # Class: (hexose transmembrane transporter activity) @@ -37350,7 +37342,7 @@ AnnotationAssertion( "GO:0015149") AnnotationAssertion(rdfs:label "hexose transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) # Class: (polysaccharide transmembrane transporter activity) @@ -37420,7 +37412,7 @@ AnnotationAssertion( "GO:0015171") AnnotationAssertion(rdfs:label "amino acid transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) # Class: (acidic amino acid transmembrane transporter activity) @@ -37834,17 +37826,6 @@ AnnotationAssertion( "ATP transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (protein-DNA complex transport) - -AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of protein-DNA complexes into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion(Annotation( "GOC:mah") "DNA-protein complex transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0015869") -AnnotationAssertion(rdfs:label "protein-DNA complex transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (acetylcholine transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions.") @@ -38209,7 +38190,7 @@ AnnotationAssertion( "Wikipedia:Phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0016310") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phosphorylation") @@ -38431,7 +38412,7 @@ EquivalentClasses( ObjectIntersection # Class: (transferase activity) -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") +AnnotationAssertion(Annotation( "EC:2.-.-.-") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") AnnotationAssertion( "EC:2.-.-.-") AnnotationAssertion(Annotation(rdfs:label "PE is converted to PS by PTDSS2") "Reactome:R-HSA-1483089") AnnotationAssertion(Annotation(rdfs:label "PC is converted to PS by PTDSS1") "Reactome:R-HSA-1483186") @@ -38465,7 +38446,7 @@ SubClassOf( (phosphotransferase activity, alcohol group as acceptor) -AnnotationAssertion(Annotation( "GOC:jl") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).") +AnnotationAssertion(Annotation( "EC:2.7.1.-") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).") AnnotationAssertion( "EC:2.7.1.-") AnnotationAssertion(Annotation(rdfs:label "abacavir + AMP => abacavir monophosphate + adenosine") "Reactome:R-HSA-2161193") AnnotationAssertion( "molecular_function") @@ -38623,6 +38604,9 @@ SubClassOf( (nuclear receptor binding) AnnotationAssertion(Annotation( "PMID:7776974") "Binding to a nuclear receptor protein. Nuclear receptor proteins are DNA-binding transcription factors which are regulated by binding to a ligand.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "GO:0035257") AnnotationAssertion( "GO:0035258") AnnotationAssertion( "steroid hormone receptor binding") @@ -38633,6 +38617,15 @@ AnnotationAssertion( "GO:0016922") AnnotationAssertion(rdfs:label "nuclear receptor binding") SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (peptide hormone binding) @@ -38711,11 +38704,23 @@ SubClassOf( (stem cell division) AnnotationAssertion(Annotation( "GOC:jid") Annotation( "ISBN:0582227089") "The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "stem cell renewal") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0017145") AnnotationAssertion(rdfs:label "stem cell division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (negative regulation of translation) @@ -38754,7 +38759,7 @@ AnnotationAssertion(Annotation( "RESID:AA0039") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0018108") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peptidyl-tyrosine phosphorylation") SubClassOf( ) SubClassOf( ) @@ -38790,7 +38795,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:go_curators") "The modification of peptidyl-tyrosine.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0018212") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peptidyl-tyrosine modification") SubClassOf( ) @@ -42027,7 +42032,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_cardio") Annotation( "GOC:mtg_transport") "Any process that modulates the frequency, rate or extent of transmembrane transporter activity.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022898") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -42711,8 +42716,9 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mah") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27107"^^xsd:anyURI) -AnnotationAssertion( "MetaCyc:PWY-6572") -AnnotationAssertion( "MetaCyc:PWY-6573") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28527"^^xsd:anyURI) +AnnotationAssertion(Annotation( "skos:narrowMatch") "MetaCyc:PWY-6572") +AnnotationAssertion(Annotation( "skos:narrowMatch") "MetaCyc:PWY-6573") AnnotationAssertion( "chondroitin sulfate breakdown") AnnotationAssertion( "chondroitin sulfate catabolism") AnnotationAssertion( "chondroitin sulfate degradation") @@ -45361,7 +45367,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "nuclease regulator activity") AnnotationAssertion( "GO:0032069") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of nuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -45373,7 +45379,7 @@ AnnotationAssertion( "DNase regulator") AnnotationAssertion( "deoxyribonuclease regulator") AnnotationAssertion( "GO:0032070") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of deoxyribonuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -45388,7 +45394,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "nuclease inhibitor") AnnotationAssertion( "GO:0032074") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of nuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -45404,7 +45410,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "nuclease activator") AnnotationAssertion( "GO:0032075") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of nuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -45420,7 +45426,7 @@ AnnotationAssertion( "DNase inhibitor") AnnotationAssertion( "deoxyribonuclease inhibitor") AnnotationAssertion( "GO:0032076") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of deoxyribonuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -45437,7 +45443,7 @@ AnnotationAssertion( "DNase activator") AnnotationAssertion( "deoxyribonuclease activator") AnnotationAssertion( "GO:0032077") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of deoxyribonuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -46275,7 +46281,7 @@ SubClassOf( "GOC:mah") "Any process that modulates the activity of a transporter.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032409") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -46288,7 +46294,7 @@ AnnotationAssertion( "inhibition of transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032410") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -46303,7 +46309,7 @@ AnnotationAssertion( "stimulation of transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032411") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -46315,7 +46321,7 @@ AnnotationAssertion( "GOC:tb") "regulation of ion transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032412") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of monoatomic ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -46329,7 +46335,7 @@ AnnotationAssertion(Annotation( "inhibition of ion transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032413") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -46345,7 +46351,7 @@ AnnotationAssertion( "stimulation of ion transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032414") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -47605,7 +47611,7 @@ AnnotationAssertion( "inhibition of ATPase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032780") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of ATP-dependent activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -47622,7 +47628,7 @@ AnnotationAssertion( "stimulation of ATPase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032781") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of ATP-dependent activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -48445,16 +48451,6 @@ AnnotationAssertion(rdfs:label "prot EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (protein-DNA complex disassembly) - -AnnotationAssertion(Annotation( "GOC:mah") "The disaggregation of a protein-DNA complex into its constituent components.") -AnnotationAssertion(Annotation( "GOC:mah") "DNA-protein complex disassembly") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032986") -AnnotationAssertion(rdfs:label "protein-DNA complex disassembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (protein-lipid complex disassembly) AnnotationAssertion(Annotation( "GOC:mah") "The disaggregation of a protein-lipid complex into its constituent components.") @@ -48513,19 +48509,6 @@ SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) -# Class: (protein-DNA complex) - -AnnotationAssertion(Annotation( "GOC:mah") "A macromolecular complex containing both protein and DNA molecules.") -AnnotationAssertion(Annotation( "GOC:mah") "DNA-protein complex") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0032993") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here.") -AnnotationAssertion(rdfs:label "protein-DNA complex") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (protein-lipid complex) AnnotationAssertion(Annotation( "GOC:mah") "A macromolecular complex containing separate protein and lipid molecules. Separate in this context means not covalently bound to each other.") @@ -49474,7 +49457,7 @@ AnnotationAssertion( "kinase inhibitor") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033673") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -49489,7 +49472,7 @@ AnnotationAssertion( "stimulation of kinase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033674") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -52225,6 +52208,9 @@ SubClassOf( (glomerular endothelium fenestra) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "MP:0011454") Annotation( "PMID:19129259") "A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "bf") AnnotationAssertion( "2011-12-12T10:53:24Z") AnnotationAssertion(Annotation( "PMID:19129259") "GEnC fenestration") @@ -52233,6 +52219,15 @@ AnnotationAssertion( "GO:0036053") AnnotationAssertion(rdfs:label "glomerular endothelium fenestra") SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (direct ossification) @@ -53965,7 +53960,7 @@ AnnotationAssertion(Annotation( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042325") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -53980,7 +53975,7 @@ AnnotationAssertion( "inhibition of phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042326") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -54325,7 +54320,6 @@ AnnotationAssertion( "GO:0042430") AnnotationAssertion(rdfs:label "indole-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (indole-containing compound biosynthetic process) @@ -55487,7 +55481,7 @@ AnnotationAssertion( "upregulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043085") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -55508,7 +55502,7 @@ AnnotationAssertion( "negative regulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043086") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -55745,10 +55739,12 @@ SubClassOf( (membrane-bounded organelle) AnnotationAssertion(Annotation( "GOC:go_curators") "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28153"^^xsd:anyURI) AnnotationAssertion( "NIF_Subcellular:sao414196390") AnnotationAssertion( "membrane-enclosed organelle") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0043227") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "membrane-bounded organelle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -55758,11 +55754,13 @@ DisjointClasses( "GOC:go_curators") "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21881"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28153"^^xsd:anyURI) AnnotationAssertion( "NIF_Subcellular:sao1456184038") AnnotationAssertion( "non-membrane-enclosed organelle") AnnotationAssertion( "cellular_component") AnnotationAssertion( "biological condensate") AnnotationAssertion( "GO:0043228") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "non-membrane-bounded organelle") SubClassOf( ) @@ -55770,8 +55768,10 @@ SubClassOf( (intracellular organelle) AnnotationAssertion(Annotation( "GOC:go_curators") "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28153"^^xsd:anyURI) AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0043229") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intracellular organelle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -56771,7 +56771,7 @@ AnnotationAssertion(Annotation( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043412") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macromolecule modification") SubClassOf( ) @@ -56829,7 +56829,7 @@ AnnotationAssertion( "negative regulation of thyroid hormone receptor activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043433") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of DNA-binding transcription factor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -56877,7 +56877,7 @@ AnnotationAssertion( "regulation of adenosinetriphosphatase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043462") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of ATP-dependent activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -57052,7 +57052,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:bf") "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043549") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -57460,10 +57460,12 @@ SubClassOf( (cellular component biogenesis) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mah") "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "GO:0071843") AnnotationAssertion( "cellular component biogenesis at cellular level") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044085") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component biogenesis") SubClassOf( ) @@ -57532,7 +57534,7 @@ AnnotationAssertion( "2009-04-21T04:11:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044093") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of molecular function") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -58050,6 +58052,9 @@ SubClassOf( (innate immune response) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:ebc") Annotation( "GOC:mtg_sensu") Annotation( "GO_REF:0000022") "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "GO:0002226") AnnotationAssertion( "Wikipedia:Innate_immune_system") AnnotationAssertion(Annotation( "GOC:pg") "innate immunity") @@ -58059,6 +58064,15 @@ AnnotationAssertion( "innate immune response") SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (regulation of innate immune response) @@ -60852,7 +60866,7 @@ SubClassOf( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of protein kinase activity.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0045859") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of protein kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -60866,7 +60880,7 @@ AnnotationAssertion( "stimulation of protein kinase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0045860") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of protein kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -66135,8 +66149,10 @@ SubClassOf( (regulation of peptidyl-tyrosine phosphorylation) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28278"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050730") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of peptidyl-tyrosine phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -66156,12 +66172,14 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of peptidyl-tyrosine phosphorylation) AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28278"^^xsd:anyURI) AnnotationAssertion( "down regulation of peptidyl-tyrosine phosphorylation") AnnotationAssertion( "down-regulation of peptidyl-tyrosine phosphorylation") AnnotationAssertion( "downregulation of peptidyl-tyrosine phosphorylation") AnnotationAssertion( "inhibition of peptidyl-tyrosine phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050732") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of peptidyl-tyrosine phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -66419,7 +66437,7 @@ AnnotationAssertion( "regulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050790") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -67076,7 +67094,6 @@ AnnotationAssertion( "GO:0050908") AnnotationAssertion(rdfs:label "detection of light stimulus involved in visual perception") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) # Class: (sensory perception of taste) @@ -67914,7 +67931,7 @@ AnnotationAssertion( "regulation of thyroid hormone receptor activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051090") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of DNA-binding transcription factor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -67936,7 +67953,7 @@ AnnotationAssertion( "stimulation of transcription factor activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051091") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of DNA-binding transcription factor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -68961,7 +68978,7 @@ AnnotationAssertion(Annotation( "hydrolase regulator") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051336") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of hydrolase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -68971,7 +68988,7 @@ AnnotationAssertion(Annotation( "transferase regulator") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051338") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -68987,7 +69004,7 @@ AnnotationAssertion( "stimulation of hydrolase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051345") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of hydrolase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69001,7 +69018,7 @@ AnnotationAssertion( "inhibition of hydrolase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051346") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of hydrolase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69016,7 +69033,7 @@ AnnotationAssertion( "stimulation of transferase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051347") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "positive regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69031,7 +69048,7 @@ AnnotationAssertion( "inhibition of transferase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051348") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "negative regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69974,7 +69991,8 @@ EquivalentClasses( ObjectIntersection # Class: (nitric-oxide synthase biosynthetic process) -AnnotationAssertion(Annotation( "EC:1.14.13.39") Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+.") +AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28860"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( "GO:0051768") AnnotationAssertion( "NO synthase biosynthesis") @@ -70619,7 +70637,6 @@ AnnotationAssertion( "GO:0052803") AnnotationAssertion(rdfs:label "imidazole-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (imidazole-containing compound catabolic process) @@ -70904,6 +70921,27 @@ AnnotationAssertion( "negative regulation of cardiac muscle tissue development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (D-glucose transmembrane transporter activity) + +AnnotationAssertion(Annotation( "GOC:jid") Annotation( "GOC:jsg") Annotation( "GOC:mah") "Enables the transfer of the D-enantiomer of the hexose monosaccharide glucose from one side of a membrane to the other.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27326"^^xsd:anyURI) +AnnotationAssertion( "GO:0015579") +AnnotationAssertion(Annotation(rdfs:label "SLC2A6,8,10,12 transport Glc from extracellular region to cytosol") "Reactome:R-HSA-429094") +AnnotationAssertion(Annotation(rdfs:label "GLUT2 (SLC2A2) transports Glc from cytosol to extracellular region") "Reactome:R-HSA-450095") +AnnotationAssertion(Annotation(rdfs:label "Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2") "Reactome:R-HSA-499981") +AnnotationAssertion(Annotation(rdfs:label "GLUT1 (SLC2A1) tetramer transports Glc from extracellular region to cytosol") "Reactome:R-HSA-5339524") +AnnotationAssertion(Annotation(rdfs:label "SLC2A1 tetramer does not transport Glc from extracellular region to cytosol") "Reactome:R-HSA-5632804") +AnnotationAssertion(Annotation(rdfs:label "Defective SLC2A10 does not transport Glc from extracellular region to cytosol") "Reactome:R-HSA-5632871") +AnnotationAssertion(Annotation(rdfs:label "SLC2A1 tetramer transports Glc from cytosol to Golgi lumen") "Reactome:R-HSA-5653873") +AnnotationAssertion(Annotation(rdfs:label "GLUT14 (SLC2A14) tetramer transports Glc from extracellular region to cytosol") "Reactome:R-HSA-8981553") +AnnotationAssertion(Annotation(rdfs:label "GLUT3 (SLC2A3) tetramer transports Glc from extracellular region to cytosol") "Reactome:R-HSA-8981564") +AnnotationAssertion(Annotation(rdfs:label "GLUT4 (SLC2A4) tetramer transports Glc from extracellular region to cytosol") "Reactome:R-HSA-8981570") +AnnotationAssertion(Annotation(rdfs:label "GLUT2 (SLC2A2) tetramer transports Glc from extracellular region to cytosol") "Reactome:R-HSA-8981574") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0055056") +AnnotationAssertion(rdfs:label "D-glucose transmembrane transporter activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (neuroblast division) AnnotationAssertion(Annotation( "PMID:11163136") Annotation( "PMID:11250167") "The process resulting in the physical partitioning and separation of a neuroblast into daughter cells. A neuroblast is any cell that will divide and give rise to a neuron.") @@ -71491,10 +71529,10 @@ SubClassOf( "GOC:mtg_MIT_16mar07") Annotation( "GOC:vw") "The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.") AnnotationAssertion( "GO:0032947") +AnnotationAssertion( "protein complex scaffold activity") +AnnotationAssertion( "protein-containing complex scaffold activity") AnnotationAssertion( "binding, bridging") AnnotationAssertion( "molecular_function") -AnnotationAssertion( "protein complex scaffold activity") -AnnotationAssertion( "protein-containing complex scaffold activity") AnnotationAssertion( "GO:0060090") AnnotationAssertion( ) AnnotationAssertion( ) @@ -75858,7 +75896,7 @@ AnnotationAssertion( "2010-04-26T02:34:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061097") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of protein tyrosine kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -75870,7 +75908,7 @@ AnnotationAssertion( "2010-04-26T02:34:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061098") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of protein tyrosine kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -75882,7 +75920,7 @@ AnnotationAssertion( "2010-04-26T02:34:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061099") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of protein tyrosine kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78642,17 +78680,6 @@ AnnotationAssertion(rdfs:label "prot EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (protein-DNA complex assembly) - -AnnotationAssertion(Annotation( "GOC:jl") "The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex.") -AnnotationAssertion(Annotation( "GOC:mah") "DNA-protein complex assembly") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0065004") -AnnotationAssertion(rdfs:label "protein-DNA complex assembly") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (protein-lipid complex assembly) AnnotationAssertion(Annotation( "GOC:jl") "The aggregation, arrangement and bonding together of proteins and lipids to form a protein-lipid complex.") @@ -78690,7 +78717,7 @@ AnnotationAssertion(Annotation( "regulation of a molecular function") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0065009") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of molecular function") @@ -80298,18 +80325,6 @@ AnnotationAssertion( "cellular response to lipoprotein particle stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (cellular response to organonitrogen compound) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2009-12-14T04:07:27Z") -AnnotationAssertion(Annotation( "GOC:mah") "cellular response to organic nitrogen") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0071417") -AnnotationAssertion(rdfs:label "cellular response to organonitrogen compound") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (cellular response to amine stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.") @@ -80657,7 +80672,7 @@ AnnotationAssertion( "2010-03-08T03:56:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071705") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nitrogen compound transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -80948,19 +80963,6 @@ AnnotationAssertion( "protein-lipid complex binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (protein-DNA complex organization) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2010-09-08T10:03:26Z") -AnnotationAssertion(Annotation( "GOC:mah") "DNA-protein complex subunit organization") -AnnotationAssertion(Annotation( "GOC:mah") "protein-DNA complex subunit organisation") -AnnotationAssertion( "protein-DNA complex subunit organization") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0071824") -AnnotationAssertion(rdfs:label "protein-DNA complex organization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (protein-lipid complex organization) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-lipid complex.") @@ -86390,17 +86392,20 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (axonemal outer doublet) +# Class: (axonemal doublet microtubule) -AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GOC:pr") Annotation( "PMID:5044758") Annotation( "PMID:5664206") Annotation( "Wikipedia:Axoneme") "Part of an axoneme consisting in a doublet microtubule. Nine of these outer doublets form the 9+0 axoneme, while the 9+2 axoneme also contains a central pair. Dynein arms attached to the doublets provide the mechanism of movement of the cilium.") +AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GOC:pr") Annotation( "PMID:5044758") Annotation( "PMID:5664206") Annotation( "Wikipedia:Axoneme") Annotation( "https://github.com/geneontology/go-ontology/issues/26128") "A cellular anatomical entity that is part of an axoneme consisting of a doublet microtubule.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26128"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2013-12-12T11:19:29Z") AnnotationAssertion( "outer doublet") +AnnotationAssertion( "axonemal outer doublet") AnnotationAssertion( "axoneme outer doublet") AnnotationAssertion( "cellular_component") +AnnotationAssertion( "DMT") AnnotationAssertion( "outer-doublet microtubules") AnnotationAssertion( "GO:0097545") -AnnotationAssertion(rdfs:label "axonemal outer doublet") +AnnotationAssertion(rdfs:label "axonemal doublet microtubule") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -87040,18 +87045,19 @@ AnnotationAssertion( "carbohydrate import across plasma membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -# Class: (glucose import across plasma membrane) +# Class: (D-glucose import across plasma membrane) -AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of glucose from outside of a cell, across the plasma membrane and into the cytosol.") +AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of D-glucose from outside of a cell, across the plasma membrane and into the cytosol.") AnnotationAssertion( "al") AnnotationAssertion( "2012-12-06T14:54:07Z") AnnotationAssertion( "GO:0061490") AnnotationAssertion( "GO:1990821") +AnnotationAssertion( "glucose import across plasma membrane") AnnotationAssertion( "glucose import into cell") AnnotationAssertion( "high affinity glucose import") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098708") -AnnotationAssertion(rdfs:label "glucose import across plasma membrane") +AnnotationAssertion(rdfs:label "D-glucose import across plasma membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (iron ion import across plasma membrane) @@ -87616,7 +87622,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:dos") "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity involved in synaptic transmission. Modulation may be via an effect on ligand affinity, or effector function such as ion selectivity or pore opening/closing in ionotropic receptors.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098962") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of postsynaptic neurotransmitter receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -88268,7 +88274,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:dos") "The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099531") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presynaptic process involved in chemical synaptic transmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -88516,7 +88522,7 @@ SubClassOf( "GOC:dos") "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity. Modulation may be via an effect on ligand affinity, or effector function such as ion selectivity or pore opening/closing in ionotropic receptors.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099601") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of neurotransmitter receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -89045,7 +89051,7 @@ AnnotationAssertion( "2018-07-06T18:53:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110112") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of lipid transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -89057,7 +89063,7 @@ AnnotationAssertion( "2018-07-06T19:14:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110113") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of lipid transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -89069,7 +89075,7 @@ AnnotationAssertion( "2018-07-06T19:21:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110114") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of lipid transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -92373,7 +92379,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of potassium transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901016") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of potassium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -92394,7 +92400,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of potassium ion transmembrane transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901017") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of potassium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -92415,7 +92421,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of potassium ion transmembrane transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901018") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of potassium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -92427,7 +92433,7 @@ AnnotationAssertion( "2012-06-15T07:54:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901019") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of calcium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -92443,7 +92449,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of calcium ion transmembrane transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901020") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of calcium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -92459,7 +92465,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of calcium ion transmembrane transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901021") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of calcium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -92509,7 +92515,10 @@ EquivalentClasses( ObjectIntersection # Class: (insulin metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways involving insulin.") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "pm") AnnotationAssertion( "2012-07-13T12:32:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "insulin metabolism") @@ -92518,9 +92527,18 @@ AnnotationAssertion( "insulin metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (insulin catabolic process) @@ -92589,7 +92607,6 @@ AnnotationAssertion( "GO:1901160") AnnotationAssertion(rdfs:label "primary amino compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (primary amino compound catabolic process) @@ -93251,7 +93268,7 @@ AnnotationAssertion( "GO:1901505") AnnotationAssertion(rdfs:label "carbohydrate derivative transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) # Class: (regulation of endothelial tube morphogenesis) @@ -93374,51 +93391,6 @@ AnnotationAssertion( "positive regulation of endothelial cell development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (organonitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways involving organonitrogen compound.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "pr") -AnnotationAssertion( "2012-11-04T15:17:52Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901564") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organonitrogen compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (organonitrogen compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "pr") -AnnotationAssertion( "2012-11-04T15:17:56Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901565") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organonitrogen compound catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (organonitrogen compound biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the formation of organonitrogen compound.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "pr") -AnnotationAssertion( "2012-11-04T15:18:00Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound anabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound biosynthesis") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901566") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organonitrogen compound biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (dendritic microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "NIF_Subcellular:sao110773650") "Any microtubule in a dendrite, a neuron projection.") @@ -95400,31 +95372,10 @@ AnnotationAssertion(Annotation( "PMID:22095752") "regulation of aquaporin permeability") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902427") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of water channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (negative regulation of water channel activity) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of water channel activity.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2013-09-23T12:56:40Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of water channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of water channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of water channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of aquaporin") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of aquaporin") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of aquaporin") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of aquaporin") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of water channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of aquaporin") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1902428") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of water channel activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (positive regulation of water channel activity) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:nhn") Annotation( "PMID:22095752") "Any process that activates or increases the frequency, rate or extent of water channel activity.") @@ -95442,7 +95393,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of aquaporin") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902429") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of water channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -97490,26 +97441,11 @@ AnnotationAssertion( "2014-05-22T14:46:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903048") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of acetylcholine-gated cation channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of acetylcholine-gated cation channel activity) - -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000059") Annotation( "PMID:21718690") "Any process that stops, prevents or reduces the frequency, rate or extent of acetylcholine-gated cation channel activity.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2014-05-22T14:47:00Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of acetylcholine-gated cation channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of acetylcholine-gated cation channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of acetylcholine-gated cation channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of acetylcholine-gated cation channel activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1903049") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of acetylcholine-gated cation channel activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of proteolysis involved in protein catabolic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:18307834") "Any process that modulates the frequency, rate or extent of proteolysis involved in cellular catabolic process.") @@ -100554,7 +100490,10 @@ SubClassOf( (epithelial cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000085") Annotation( "PMID:19137015") "Any apoptotic process in an epithelial cell.") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-06T22:27:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "epitheliocyte apoptotic process") @@ -100565,9 +100504,18 @@ AnnotationAssertion( "epithelial cell apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (regulation of collagen fibril organization) @@ -101558,7 +101506,7 @@ AnnotationAssertion( "GOC:TermGenie") "regulation of iron-specific channel activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904254") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of iron ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -101585,39 +101533,11 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of iron-specific channel activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904255") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of iron ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (positive regulation of iron ion transmembrane transporter activity) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000059") Annotation( "PMID:15514116") "Any process that activates or increases the frequency, rate or extent of an iron transmembrane transporter activity.") -AnnotationAssertion( "kom") -AnnotationAssertion( "2015-05-20T14:05:12Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of iron cation channel activity") -AnnotationAssertion( "positive regulation of iron channel activity") -AnnotationAssertion( "positive regulation of iron transmembrane transporter activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of iron-specific channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of iron cation channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of iron channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of iron-specific channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of iron cation channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of iron channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of iron-specific channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of iron cation channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of iron channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of iron-specific channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of iron cation channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of iron channel activity") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of iron-specific channel activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1904256") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of iron ion transmembrane transporter activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of Schwann cell chemotaxis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16203995") "Any process that modulates the frequency, rate or extent of Schwann cell chemotaxis.") @@ -102972,16 +102892,17 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (glucose transmembrane transport) +# Class: (D-glucose transmembrane transport) -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000069") Annotation( "PMID:9090050") "The process in which glucose is transported across a membrane.") +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000069") Annotation( "PMID:9090050") "The process in which D-glucose is transported across a membrane.") AnnotationAssertion( "vw") AnnotationAssertion( "2015-09-04T17:20:16Z") AnnotationAssertion( "GO:0015758") +AnnotationAssertion( "glucose transmembrane transport") AnnotationAssertion( "biological_process") AnnotationAssertion( "glucose transport") AnnotationAssertion( "GO:1904659") -AnnotationAssertion(rdfs:label "glucose transmembrane transport") +AnnotationAssertion(rdfs:label "D-glucose transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (negative regulation of cell differentiation involved in stem cell population maintenance) @@ -110152,7 +110073,7 @@ AnnotationAssertion( "negative regulation of signalling receptor activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000272") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of signaling receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -110166,7 +110087,7 @@ AnnotationAssertion( AnnotationAssertion( "positive regulation of signalling receptor activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000273") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of signaling receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -110362,7 +110283,7 @@ AnnotationAssertion( "2011-01-18T10:14:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000312") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of kainate selective glutamate receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -111716,7 +111637,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GOC:obol") "regulation of sodium transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000649") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of sodium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -111729,7 +111650,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of sodium transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000650") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of sodium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -111742,7 +111663,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of sodium transporter activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000651") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of sodium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -112247,7 +112168,7 @@ AnnotationAssertion( "2011-07-15T10:56:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000825") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of androgen receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -113336,7 +113257,7 @@ AnnotationAssertion(Annotation( "GOC:obol") "regulation of nonselective cation channel activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001257") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of cation channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -113350,7 +113271,7 @@ AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of nonselective cation channel activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001258") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of cation channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -113364,7 +113285,7 @@ AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of nonselective cation channel activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001259") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of cation channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 440e8a95b..66b769be1 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-09-13") + +Annotation(owl:versionInfo "2024-09-19") Declaration(Class()) Declaration(Class())