From 32ae5a042b3381d6b0b4d613455ef18d378e0428 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 15 Jun 2023 17:04:46 +0100 Subject: [PATCH 1/5] Addresses #2020 NTR alveolar macrophages Fixes #2020 NTR alveolar macrophages --- src/ontology/cl-edit.owl | 39 ++++++++++++++++++++++++++++++++++++--- 1 file changed, 36 insertions(+), 3 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 3cfb63d28..a0885f965 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -2971,6 +2971,9 @@ Declaration(Class(obo:CL_4033037)) Declaration(Class(obo:CL_4033038)) Declaration(Class(obo:CL_4033039)) Declaration(Class(obo:CL_4033040)) +Declaration(Class(obo:CL_4033041)) +Declaration(Class(obo:CL_4033042)) +Declaration(Class(obo:CL_4033043)) Declaration(Class(obo:CL_4033049)) Declaration(Class(obo:CL_4033050)) Declaration(Class(obo:CL_4040000)) @@ -3926,8 +3929,8 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation( AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "BTO:0000452") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "CALOHA:TS-0362") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "FMA:63877") -AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "VHOG:0001482") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "NCIT:C12482") +AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000057 "VHOG:0001482") AnnotationAssertion(rdfs:comment obo:CL_0000057 "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.") AnnotationAssertion(rdfs:label obo:CL_0000057 "fibroblast") SubClassOf(obo:CL_0000057 obo:CL_0002320) @@ -8403,9 +8406,9 @@ AnnotationAssertion(owl:deprecated obo:CL_0000585 "true"^^xsd:boolean) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D005854") obo:IAO_0000115 obo:CL_0000586 "The reproductive cell in multicellular organisms.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "BTO:0000535") +AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "NCIT:C12597") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "VHOG:0001534") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "WBbt:0006796") -AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000586 "NCIT:C12597") AnnotationAssertion(rdfs:label obo:CL_0000586 "germ cell") SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000586 obo:CL_0000039) SubClassOf(obo:CL_0000586 ObjectSomeValuesFrom(obo:RO_0002216 obo:GO_0009566)) @@ -27711,9 +27714,9 @@ SubClassOf(obo:CL_1001451 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000004 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MP:0008462") Annotation(oboInOwl:hasDbXref "doi:10.1073/pnas.242428599") obo:IAO_0000115 obo:CL_1001474 "An inhibitory, GABAergic projection neuron in the striatum that integrates glutamatergic signals arising from the cerebral cortex and thalamus.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1001474 "BTO:0004778") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0021773") oboInOwl:hasExactSynonym obo:CL_1001474 "striatal medium spiny neuron") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1073/pnas.242428599") oboInOwl:hasExactSynonym obo:CL_1001474 "gamma-aminobutyric acid (GABA)ergic spiny projection neuron") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1073/pnas.242428599") oboInOwl:hasExactSynonym obo:CL_1001474 "gamma-aminobutyric acid ergic spiny projection neuron") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0021773") oboInOwl:hasExactSynonym obo:CL_1001474 "striatal medium spiny neuron") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "BTO:0004778") oboInOwl:hasRelatedSynonym obo:CL_1001474 "medium-sized densely spiny neuron") AnnotationAssertion(rdfs:label obo:CL_1001474 "medium spiny neuron") SubClassOf(obo:CL_1001474 obo:CL_0000540) @@ -31484,6 +31487,36 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27776108") oboInOwl:hasE AnnotationAssertion(rdfs:label obo:CL_4033040 "lung resident memory CD8-positive, CD103-positive, alpha-beta T cell") EquivalentClasses(obo:CL_4033040 ObjectIntersectionOf(obo:CL_4033039 ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001010))) +# Class: obo:CL_4033041 (alveolar macrophage CCL3-positive) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2022.03.10.483747") obo:IAO_0000115 obo:CL_4033041 "An alveolar macrophage that expresses CCL3.") +AnnotationAssertion( obo:CL_4033041 ) +AnnotationAssertion( obo:CL_4033041 ) +AnnotationAssertion( obo:CL_4033041 "2023-06-15T12:53:08Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:CL_4033041 "alveolar macrophage CCL3-positive") +SubClassOf(obo:CL_4033041 obo:CL_0000583) + +# Class: obo:CL_4033042 (alveolar macrophage metallothionein-positive) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2022.03.10.483747") obo:IAO_0000115 obo:CL_4033042 "An alveolar macrophage that expresses metallothionein.") +AnnotationAssertion( obo:CL_4033042 ) +AnnotationAssertion( obo:CL_4033042 ) +AnnotationAssertion( obo:CL_4033042 "2023-06-15T12:55:34Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2022.03.10.483747") oboInOwl:hasExactSynonym obo:CL_4033042 "alveolar macrophage MT-positive") +AnnotationAssertion(rdfs:label obo:CL_4033042 "alveolar macrophage metallothionein-positive") +SubClassOf(obo:CL_4033042 obo:CL_0000583) + +# Class: obo:CL_4033043 (lung interstitial macrophage) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33382972") Annotation(oboInOwl:hasDbXref "PMID:35017701") Annotation(oboInOwl:hasDbXref "PMID:36211428") obo:IAO_0000115 obo:CL_4033043 "A macrophage that is part of the lung connective tissue (pulmonary interstitium). This cell performs tissue remodeling and contributes to barrier immunity through antigen presentation.") +AnnotationAssertion( obo:CL_4033043 ) +AnnotationAssertion( obo:CL_4033043 ) +AnnotationAssertion( obo:CL_4033043 "2023-06-15T12:58:11Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36211428") Annotation(oboInOwl:hasSynonymType ) oboInOwl:hasRelatedSynonym obo:CL_4033043 "lung IM") +AnnotationAssertion(rdfs:label obo:CL_4033043 "lung interstitial macrophage") +SubClassOf(obo:CL_4033043 obo:CL_0000235) +SubClassOf(obo:CL_4033043 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000114)) + # Class: obo:CL_4033049 (taste receptor cell of tongue) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1111/j.1096-3642.1981.tb01137.x") Annotation(oboInOwl:hasDbXref "PMID:10052456") Annotation(oboInOwl:hasDbXref "PMID:28655883") Annotation(oboInOwl:hasDbXref "http://www.nejohnston.org/Birds/documents/AvianTongues_Johnston.pdf") obo:IAO_0000115 obo:CL_4033049 "A taste receptor cell that is part of a taste bud of a tongue.") From cdffa02e9411d810de244e4690a5d0c57dc40750 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 15 Jun 2023 18:32:06 +0100 Subject: [PATCH 2/5] Update references from preprint to published article --- 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 a0885f965..bf274802f 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31489,7 +31489,7 @@ EquivalentClasses(obo:CL_4033040 ObjectIntersectionOf(obo:CL_4033039 ObjectSomeV # Class: obo:CL_4033041 (alveolar macrophage CCL3-positive) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2022.03.10.483747") obo:IAO_0000115 obo:CL_4033041 "An alveolar macrophage that expresses CCL3.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") obo:IAO_0000115 obo:CL_4033041 "An alveolar macrophage that expresses CCL3.") AnnotationAssertion( obo:CL_4033041 ) AnnotationAssertion( obo:CL_4033041 ) AnnotationAssertion( obo:CL_4033041 "2023-06-15T12:53:08Z"^^xsd:dateTime) @@ -31498,11 +31498,11 @@ SubClassOf(obo:CL_4033041 obo:CL_0000583) # Class: obo:CL_4033042 (alveolar macrophage metallothionein-positive) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2022.03.10.483747") obo:IAO_0000115 obo:CL_4033042 "An alveolar macrophage that expresses metallothionein.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") obo:IAO_0000115 obo:CL_4033042 "An alveolar macrophage that expresses metallothionein.") AnnotationAssertion( obo:CL_4033042 ) AnnotationAssertion( obo:CL_4033042 ) AnnotationAssertion( obo:CL_4033042 "2023-06-15T12:55:34Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2022.03.10.483747") oboInOwl:hasExactSynonym obo:CL_4033042 "alveolar macrophage MT-positive") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") oboInOwl:hasExactSynonym obo:CL_4033042 "alveolar macrophage MT-positive") AnnotationAssertion(rdfs:label obo:CL_4033042 "alveolar macrophage metallothionein-positive") SubClassOf(obo:CL_4033042 obo:CL_0000583) From c5ec5c25161cfe49bc73cf4a2320d79ab5b4cd1d Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Fri, 16 Jun 2023 14:00:27 +0100 Subject: [PATCH 3/5] Update changes --- src/ontology/cl-edit.owl | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index bf274802f..3559575b8 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3160,7 +3160,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to") -# Annotation Property: obo:IAO_0000700 (has ontology root term) +# Annotation Property: obo:IAO_0000700 (preferred_root) AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root") @@ -31487,23 +31487,27 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27776108") oboInOwl:hasE AnnotationAssertion(rdfs:label obo:CL_4033040 "lung resident memory CD8-positive, CD103-positive, alpha-beta T cell") EquivalentClasses(obo:CL_4033040 ObjectIntersectionOf(obo:CL_4033039 ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001010))) -# Class: obo:CL_4033041 (alveolar macrophage CCL3-positive) +# Class: obo:CL_4033041 (CCL3-positive alveolar macrophage) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") obo:IAO_0000115 obo:CL_4033041 "An alveolar macrophage that expresses CCL3.") AnnotationAssertion( obo:CL_4033041 ) AnnotationAssertion( obo:CL_4033041 ) AnnotationAssertion( obo:CL_4033041 "2023-06-15T12:53:08Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label obo:CL_4033041 "alveolar macrophage CCL3-positive") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") oboInOwl:hasExactSynonym obo:CL_4033041 "alveolar macrophage CCL3-positive") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") rdfs:comment obo:CL_4033041 "In humans, a CCL3-positive alveolar macrophage has been noted to have enriched gene expression of the following: CD53, PTPRC, CORO1A, FCER1G, C1orf162, CLEC7A, CCL20, and FAM89A.") +AnnotationAssertion(rdfs:label obo:CL_4033041 "CCL3-positive alveolar macrophage") SubClassOf(obo:CL_4033041 obo:CL_0000583) -# Class: obo:CL_4033042 (alveolar macrophage metallothionein-positive) +# Class: obo:CL_4033042 (metallothionein-positive alveolar macrophage) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") obo:IAO_0000115 obo:CL_4033042 "An alveolar macrophage that expresses metallothionein.") AnnotationAssertion( obo:CL_4033042 ) AnnotationAssertion( obo:CL_4033042 ) AnnotationAssertion( obo:CL_4033042 "2023-06-15T12:55:34Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") oboInOwl:hasExactSynonym obo:CL_4033042 "alveolar macrophage MT-positive") -AnnotationAssertion(rdfs:label obo:CL_4033042 "alveolar macrophage metallothionein-positive") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") oboInOwl:hasExactSynonym obo:CL_4033042 "alveolar macrophage metallothionein-positive") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") rdfs:comment obo:CL_4033042 "In humans, an MT-positive alveolar macrophage has been noted to have enriched gene expression of the following: CD53, PTPRC, CORO1A, FCER1G, C1orf162, CLEC7A, MT1M, CCL18, and MT1E.") +AnnotationAssertion(rdfs:label obo:CL_4033042 "metallothionein-positive alveolar macrophage") SubClassOf(obo:CL_4033042 obo:CL_0000583) # Class: obo:CL_4033043 (lung interstitial macrophage) From b8b01382f219e916eebb726e0318b12667de9035 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Fri, 16 Jun 2023 16:19:09 +0100 Subject: [PATCH 4/5] Remove comments, added import PR:000002123 and refreshed imports --- src/ontology/cl-edit.owl | 4 +- src/ontology/imports/merged_import.owl | 876 ++++++++++++++++--------- src/ontology/imports/pr_terms.txt | 1 + src/patterns/definitions.owl | 5 +- 4 files changed, 561 insertions(+), 325 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 3559575b8..382af0ad7 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3017,6 +3017,7 @@ Declaration(Class(obo:PR_000001224)) Declaration(Class(obo:PR_000001243)) Declaration(Class(obo:PR_000001244)) Declaration(Class(obo:PR_000002030)) +Declaration(Class(obo:PR_000002123)) Declaration(Class(obo:PR_000003264)) Declaration(Class(obo:PR_000005444)) Declaration(Class(obo:PR_000005460)) @@ -31494,9 +31495,9 @@ AnnotationAssertion( obo:CL_4033041 obo:CL_4033041 ) AnnotationAssertion( obo:CL_4033041 "2023-06-15T12:53:08Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") oboInOwl:hasExactSynonym obo:CL_4033041 "alveolar macrophage CCL3-positive") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") rdfs:comment obo:CL_4033041 "In humans, a CCL3-positive alveolar macrophage has been noted to have enriched gene expression of the following: CD53, PTPRC, CORO1A, FCER1G, C1orf162, CLEC7A, CCL20, and FAM89A.") AnnotationAssertion(rdfs:label obo:CL_4033041 "CCL3-positive alveolar macrophage") SubClassOf(obo:CL_4033041 obo:CL_0000583) +SubClassOf(obo:CL_4033041 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000002123)) # Class: obo:CL_4033042 (metallothionein-positive alveolar macrophage) @@ -31506,7 +31507,6 @@ AnnotationAssertion( obo:CL_4033042 obo:CL_4033042 "2023-06-15T12:55:34Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") oboInOwl:hasExactSynonym obo:CL_4033042 "alveolar macrophage MT-positive") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") oboInOwl:hasExactSynonym obo:CL_4033042 "alveolar macrophage metallothionein-positive") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37291214") rdfs:comment obo:CL_4033042 "In humans, an MT-positive alveolar macrophage has been noted to have enriched gene expression of the following: CD53, PTPRC, CORO1A, FCER1G, C1orf162, CLEC7A, MT1M, CCL18, and MT1E.") AnnotationAssertion(rdfs:label obo:CL_4033042 "metallothionein-positive alveolar macrophage") SubClassOf(obo:CL_4033042 obo:CL_0000583) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index a9da226e9..7c128191d 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,10 +7,8 @@ Prefix(rdfs:=) Ontology( - - -Annotation(owl:versionInfo "2023-06-14") - + +Annotation(owl:versionInfo "2023-06-16") Declaration(Class()) Declaration(Class()) @@ -51,6 +49,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -103,7 +102,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -137,6 +138,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -147,11 +151,13 @@ 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()) Declaration(Class()) @@ -161,6 +167,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -721,6 +729,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1433,7 +1442,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1476,6 +1484,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1486,6 +1495,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1551,6 +1561,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1602,6 +1613,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1825,8 +1837,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1872,6 +1882,12 @@ 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()) @@ -1962,7 +1978,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2087,7 +2102,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2226,6 +2240,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2250,6 +2265,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2355,7 +2372,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3148,6 +3164,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3764,6 +3781,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3847,6 +3865,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4123,6 +4142,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4801,7 +4823,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5619,6 +5640,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6947,6 +6969,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7318,7 +7343,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7799,6 +7823,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8481,7 +8508,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13806,7 +13832,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -13911,7 +13936,6 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -13981,6 +14005,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14316,10 +14341,6 @@ SubAnnotationPropertyOf( SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -19367,6 +19388,8 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0001505") AnnotationAssertion(rdfs:label "regulation of neurotransmitter levels") +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (action potential) @@ -19555,6 +19578,21 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (G protein-coupled ADP receptor activity) + +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:signaling") Annotation( "PMID:11196645") "Combining with ADP and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.") +AnnotationAssertion( "GO:0045032") +AnnotationAssertion( "ADP receptor activity") +AnnotationAssertion( "ADP-activated nucleotide receptor activity") +AnnotationAssertion( "K101 receptor") +AnnotationAssertion(Annotation( "GOC:mah") "platelet ADP receptor activity") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "ADP-activated adenosine receptor activity") +AnnotationAssertion( "GO:0001621") +AnnotationAssertion(rdfs:label "G protein-coupled ADP receptor activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (osteoblast differentiation) AnnotationAssertion(Annotation( "CL:0000062") Annotation( "GOC:jid") Annotation( "GO_REF:0000034") "The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.") @@ -20063,6 +20101,8 @@ AnnotationAssertion( "cell activation") SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (leukocyte homeostasis) @@ -20713,7 +20753,6 @@ AnnotationAssertion(rdfs:label "T ce EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (regulation of T cell mediated cytotoxicity) @@ -27733,12 +27772,16 @@ EquivalentClasses( ObjectIntersection # Class: (establishment of cell polarity involved in ameboidal cell migration) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell.") +AnnotationAssertion( ) AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-08T04:50:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003365") AnnotationAssertion(rdfs:label "establishment of cell polarity involved in ameboidal cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (establishment or maintenance of cytoskeleton polarity involved in ameboidal cell migration) @@ -28145,18 +28188,6 @@ AnnotationAssertion( "catalytic activity") SubClassOf( ) -# Class: (ATP-dependent peptidase activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Catalysis of the hydrolysis of peptide bonds, driven by ATP hydrolysis.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21612"^^xsd:anyURI) -AnnotationAssertion( "GO:0004280") -AnnotationAssertion(Annotation(rdfs:label "pPR-AP:pAP cleaves the MCP:pPR-AP:pAP Complex") "Reactome:R-HSA-9698929") -AnnotationAssertion( "molecular_function") -AnnotationAssertion(Annotation( "GOC:mah") "ATP-dependent proteolysis") -AnnotationAssertion( "GO:0004176") -AnnotationAssertion(rdfs:label "ATP-dependent peptidase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (nuclease activity) AnnotationAssertion(Annotation( "ISBN:0198547684") "Catalysis of the hydrolysis of ester linkages within nucleic acids.") @@ -28214,7 +28245,7 @@ AnnotationAssertion( "GO:0004696") AnnotationAssertion( "GO:0004700") AnnotationAssertion( "GO:0106311") -AnnotationAssertion(Annotation( "skos:narrowMatch") "EC:2.7.11.1") +AnnotationAssertion(Annotation( "skos:exactMatch") "EC:2.7.11.1") AnnotationAssertion(Annotation(rdfs:label "PDPK1 phosphorylates AKT2") "Reactome:R-HSA-109702") AnnotationAssertion(Annotation(rdfs:label "MAPK3,(MAPK1) phosphorylates GRB2-1:SOS1:p-Y427-SHC1") "Reactome:R-HSA-109822") AnnotationAssertion(Annotation(rdfs:label "MAPK3,(MAPK1) phosphorylates GRB2-1:SOS1:p-Y-IRS1,p-Y-IRS2") "Reactome:R-HSA-109823") @@ -28697,8 +28728,6 @@ AnnotationAssertion(Annotation(rdfs:label "MAPKAPK2 phosphorylates RIPK1 at S320 AnnotationAssertion(Annotation(rdfs:label "TBK1, IKBKE phosphorylate RIPK1 at T189") "Reactome:R-HSA-9817397") AnnotationAssertion(Annotation(rdfs:label "CHUK, IKBKB phosphorylate RIPK1 at S25") "Reactome:R-HSA-9818789") AnnotationAssertion(Annotation(rdfs:label "ULK1 phosphorylates RIPK1 at S357") "Reactome:R-HSA-9819106") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "protein kinase (phosphorylating) activity") -AnnotationAssertion(Annotation( "EC:2.7.11.1") "protein phosphokinase activity") AnnotationAssertion(Annotation( "EC:2.7.11.1") "protein serine kinase activity") AnnotationAssertion( "protein threonine kinase activity") AnnotationAssertion(Annotation( "EC:2.7.11.1") "protein-serine kinase activity") @@ -29100,6 +29129,11 @@ AnnotationAssertion( "GO:0004713") AnnotationAssertion(rdfs:label "protein tyrosine kinase activity") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (transmembrane receptor protein tyrosine kinase activity) @@ -29620,6 +29654,7 @@ AnnotationAssertion(rdfs:label "L-gl EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lipid transporter activity) @@ -29653,6 +29688,8 @@ AnnotationAssertion( "GO:0005326") AnnotationAssertion(rdfs:label "neurotransmitter transmembrane transporter activity") SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (organic acid transmembrane transporter activity) @@ -29663,6 +29700,17 @@ AnnotationAssertion(rdfs:label "orga EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (ATP transmembrane transporter activity) + +AnnotationAssertion(Annotation( "GOC:ai") "Enables the transfer of ATP, adenosine triphosphate, from one side of a membrane to the other.") +AnnotationAssertion( "GO:0005348") +AnnotationAssertion(Annotation(rdfs:label "CALHM1:CALHM3 transports ATP from the cytosol to the extracellular region") "Reactome:R-HSA-9717392") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0005347") +AnnotationAssertion(rdfs:label "ATP transmembrane transporter activity") +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.") @@ -29789,6 +29837,17 @@ AnnotationAssertion( "collagen binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (ATP binding) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.") +AnnotationAssertion(Annotation(rdfs:label "KCNJ11 tetramer:ABCC8 tetramer binds 4xATP, closing the channel") "Reactome:R-HSA-265682") +AnnotationAssertion( "Mg-ATP binding") +AnnotationAssertion( "MgATP binding") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0005524") +AnnotationAssertion(rdfs:label "ATP binding") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (glucose binding) AnnotationAssertion(Annotation( "GOC:jl") "Binding to D- or L-enantiomers of glucose.") @@ -30800,6 +30859,18 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (ADP biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the formation of ADP, adenosine 5'-diphosphate.") +AnnotationAssertion( "ADP anabolism") +AnnotationAssertion( "ADP biosynthesis") +AnnotationAssertion( "ADP formation") +AnnotationAssertion( "ADP synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006172") +AnnotationAssertion(rdfs:label "ADP biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (DNA metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.") @@ -31041,8 +31112,8 @@ AnnotationAssertion(Annotation( "GOC:bf") "protein amino acid phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006468") +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein phosphorylation") SubClassOf( ) SubClassOf( ) @@ -31056,7 +31127,7 @@ 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( ) @@ -31516,6 +31587,21 @@ AnnotationAssertion(rdfs:label "cell EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (ATP biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.") +AnnotationAssertion( "GO:0006758") +AnnotationAssertion( "GO:0006759") +AnnotationAssertion( "ATP anabolism") +AnnotationAssertion( "ATP biosynthesis") +AnnotationAssertion( "ATP formation") +AnnotationAssertion( "ATP synthesis") +AnnotationAssertion( "ATP regeneration") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006754") +AnnotationAssertion(rdfs:label "ATP biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (phosphate-containing compound metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.") @@ -32948,6 +33034,7 @@ SubClassOf( "GOC:go_curators") "The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.") AnnotationAssertion( "germ-cell development") +AnnotationAssertion( "gametogenesis") AnnotationAssertion( "primordial germ cell development") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0007281") @@ -34325,59 +34412,6 @@ AnnotationAssertion( "G protein-coupled amine receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (peptidase activity) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0815332181") "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.") -AnnotationAssertion( "GO:0070010") -AnnotationAssertion( "GO:0070011") -AnnotationAssertion( "EC:3.4.-.-") -AnnotationAssertion(Annotation(rdfs:label "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6") "Reactome:R-HSA-205112") -AnnotationAssertion(Annotation(rdfs:label "Unknown lysosomal protease degrades CBLIF:RCbl to release Cbl") "Reactome:R-HSA-3000243") -AnnotationAssertion(Annotation(rdfs:label "TCN2:RCbl is degraded to release RCbl") "Reactome:R-HSA-3000263") -AnnotationAssertion(Annotation(rdfs:label "An unknown protease degrades ACACA") "Reactome:R-HSA-3065958") -AnnotationAssertion(Annotation(rdfs:label "An unknown protease degrades hCBXs") "Reactome:R-HSA-3065959") -AnnotationAssertion(Annotation(rdfs:label "Maturation of HIV Virion") "Reactome:R-HSA-3139027") -AnnotationAssertion(Annotation(rdfs:label "Proteolytic processing of SLIT") "Reactome:R-HSA-376149") -AnnotationAssertion(Annotation(rdfs:label "An unknown protease degrades ACACB") "Reactome:R-HSA-4167501") -AnnotationAssertion(Annotation(rdfs:label "CTSG cleaves CASP1(1-404)") "Reactome:R-HSA-448678") -AnnotationAssertion(Annotation(rdfs:label "USP1 autocleavage") "Reactome:R-HSA-5655483") -AnnotationAssertion(Annotation(rdfs:label "NAPSA, CTSH, PGA3-5 cleave pro-SFTPB") "Reactome:R-HSA-5684864") -AnnotationAssertion(Annotation(rdfs:label "NAPSA, CTSH, PGA3-5 cleave pro-SFTPC") "Reactome:R-HSA-5685902") -AnnotationAssertion(Annotation(rdfs:label "DCD(63-110) is processed to DCD(63-109)") "Reactome:R-HSA-6803060") -AnnotationAssertion( "hydrolase, acting on peptide bonds") -AnnotationAssertion( "peptide hydrolase activity") -AnnotationAssertion( "protease activity") -AnnotationAssertion( "peptidase activity, acting on D-amino acid peptides") -AnnotationAssertion( "peptidase activity, acting on L-amino acid peptides") -AnnotationAssertion( "proteinase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0008233") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "peptidase activity") -SubClassOf( ) -SubClassOf( ) - -# Class: (cysteine-type peptidase activity) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE") "Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.") -AnnotationAssertion( "GO:0004220") -AnnotationAssertion(Annotation(rdfs:label "Cathepsin Z (Cathepsin X) hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-8)") "Reactome:R-HSA-2022381") -AnnotationAssertion(Annotation(rdfs:label "Autocleavage of ESPL1 (Separase)") "Reactome:R-HSA-2467775") -AnnotationAssertion(Annotation(rdfs:label "ESPL1 (Separase) cleaves centromeric cohesin") "Reactome:R-HSA-2467809") -AnnotationAssertion(Annotation(rdfs:label "USP9X deubiquitinates Ub-SNCA") "Reactome:R-HSA-5660752") -AnnotationAssertion(Annotation(rdfs:label "CASP8 cleaves N4BP1 at D424, D490") "Reactome:R-HSA-9757951") -AnnotationAssertion( "cysteine protease activity") -AnnotationAssertion( "thiol protease activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0008234") -AnnotationAssertion(rdfs:label "cysteine-type peptidase activity") -SubClassOf( ) - # Class: (regulation of G protein-coupled receptor signaling pathway) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of G protein-coupled receptor signaling pathway.") @@ -34691,6 +34725,7 @@ AnnotationAssertion( "ammonium transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "GO_REF:0000090") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (G protein-coupled peptide receptor activity) @@ -35030,6 +35065,70 @@ AnnotationAssertion(rdfs:label "glyc EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (nucleoside diphosphate metabolic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar.") +AnnotationAssertion( "nucleoside diphosphate metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009132") +AnnotationAssertion(rdfs:label "nucleoside diphosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (nucleoside diphosphate biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar.") +AnnotationAssertion( "nucleoside diphosphate anabolism") +AnnotationAssertion( "nucleoside diphosphate biosynthesis") +AnnotationAssertion( "nucleoside diphosphate formation") +AnnotationAssertion( "nucleoside diphosphate synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009133") +AnnotationAssertion(rdfs:label "nucleoside diphosphate biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (nucleoside diphosphate catabolic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar.") +AnnotationAssertion( "nucleoside diphosphate breakdown") +AnnotationAssertion( "nucleoside diphosphate catabolism") +AnnotationAssertion( "nucleoside diphosphate degradation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009134") +AnnotationAssertion(rdfs:label "nucleoside diphosphate catabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (nucleoside triphosphate metabolic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.") +AnnotationAssertion( "nucleoside triphosphate metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009141") +AnnotationAssertion(rdfs:label "nucleoside triphosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (nucleoside triphosphate biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.") +AnnotationAssertion( "nucleoside triphosphate anabolism") +AnnotationAssertion( "nucleoside triphosphate biosynthesis") +AnnotationAssertion( "nucleoside triphosphate formation") +AnnotationAssertion( "nucleoside triphosphate synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009142") +AnnotationAssertion(rdfs:label "nucleoside triphosphate biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (nucleoside triphosphate catabolic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.") +AnnotationAssertion( "nucleoside triphosphate breakdown") +AnnotationAssertion( "nucleoside triphosphate catabolism") +AnnotationAssertion( "nucleoside triphosphate degradation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009143") +AnnotationAssertion(rdfs:label "nucleoside triphosphate catabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (glucan biosynthetic process) AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.") @@ -36144,16 +36243,6 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (negative regulation of peptidase activity) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010466") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of peptidase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) - # Class: (gene expression) AnnotationAssertion(Annotation( "GOC:txnOH-2018") Annotation( "PMID:25934543") Annotation( "PMID:31580950") "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.") @@ -36186,7 +36275,7 @@ 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( ) @@ -37328,18 +37417,6 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (positive regulation of peptidase activity) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins.") -AnnotationAssertion( "tb") -AnnotationAssertion( "2009-04-27T11:54:32Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010952") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of peptidase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) - # Class: (positive regulation of protein processing) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of protein maturation by peptide bond cleavage.") @@ -38653,6 +38730,7 @@ AnnotationAssertion( "calcium ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bicarbonate transmembrane transporter activity) @@ -38664,6 +38742,7 @@ AnnotationAssertion( "bicarbonate transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bile acid transmembrane transporter activity) @@ -38837,6 +38916,15 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (ADP transmembrane transporter activity) + +AnnotationAssertion(Annotation( "GOC:ai") "Enables the transfer of ADP, adenosine diphosphate, from one side of a membrane to the other.") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0015217") +AnnotationAssertion(rdfs:label "ADP transmembrane transporter activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (water channel activity) AnnotationAssertion(Annotation( "GOC:mtg_transport") Annotation( "ISBN:0815340729") "Transport systems of this type enable facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.") @@ -38855,6 +38943,7 @@ AnnotationAssertion(rdfs:label "wate EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (channel activity) @@ -39096,6 +39185,22 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (ADP transport) + +AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of ADP, adenosine diphosphate, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0015866") +AnnotationAssertion(rdfs:label "ADP transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (ATP transport) + +AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of ATP, adenosine triphosphate, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0015867") +AnnotationAssertion(rdfs:label "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.") @@ -39413,6 +39518,7 @@ SubClassOf( ObjectSomeValuesFrom( (vesicle-mediated transport) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:mah") Annotation( "ISBN:08789310662000") "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25421"^^xsd:anyURI) AnnotationAssertion( "GO:0006899") AnnotationAssertion( "vesicle transport") AnnotationAssertion(Annotation( "GOC:mah") "vesicular transport") @@ -39429,6 +39535,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vesicle-mediated transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (regulation of striated muscle tissue development) @@ -39616,11 +39723,15 @@ SubClassOf( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:ems") Annotation( "GOC:pf") Annotation( "Wikipedia:Cell_migration") "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24787"^^xsd:anyURI) +AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Cell_migration") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0016477") AnnotationAssertion(rdfs:label "cell migration") SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (protein processing) @@ -39764,7 +39875,6 @@ AnnotationAssertion( "GO:0016755") AnnotationAssertion(rdfs:label "aminoacyltransferase activity") SubClassOf( ) -SubClassOf( ) # Class: (transferase activity, transferring phosphorus-containing groups) @@ -39924,6 +40034,11 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "ATP hydrolysis activity") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (G protein-coupled acetylcholine receptor activity) @@ -39998,6 +40113,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ribonucleoside triphosphate phosphatase activity") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nucleologenesis) @@ -40056,7 +40176,7 @@ AnnotationAssertion(Annotation( "RESID:AA0039") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0018108") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peptidyl-tyrosine phosphorylation") SubClassOf( ) SubClassOf( ) @@ -40095,8 +40215,8 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mah") "The alteration of an amino acid residue in a peptide.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0018193") +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peptidyl-amino acid modification") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -40106,7 +40226,7 @@ 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( ) @@ -40476,7 +40596,7 @@ SubClassOf( (Atg12 transferase activity) -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:12826404") "Catalysis of the transfer of ATG12 from one protein to another via the reaction X-ATG12 + Y --> Y-ATG12 + X, where both X-ATG12 and Y-ATG12 are covalent linkages.") +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:12826404") "Catalysis of the transfer of ATG12 from one protein to another via the reaction X-ATG12 + Y = Y-ATG12 + X, where both X-ATG12 and Y-ATG12 are covalent linkages.") AnnotationAssertion(Annotation(rdfs:label "ATG10 transfers ATG12 from ATG7 to ATG10") "Reactome:R-HSA-5681999") AnnotationAssertion( "APG12 conjugating enzyme activity") AnnotationAssertion( "APG12 ligase activity") @@ -40496,48 +40616,29 @@ AnnotationAssertion( "Atg12 activating enzyme activity") SubClassOf( ) -# Class: (ubiquitin-like protein peptidase activity) - -AnnotationAssertion(Annotation( "PMID:19489724") "An isopeptidase activity that cleaves ubiquitin or ubiquitin-like proteins (ULP; e.g. ATG8, ISG15, NEDD8, SUMO) from target proteins.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17398"^^xsd:anyURI) -AnnotationAssertion( "GO:0070138") -AnnotationAssertion( "GO:0140491") -AnnotationAssertion( "GO:1904454") -AnnotationAssertion( "GO:1904455") -AnnotationAssertion(Annotation( "GOC:dph") "small conjugating protein-specific isopeptidase activity") -AnnotationAssertion(Annotation( "GOC:dph") "small conjugating protein-specific protease activity") -AnnotationAssertion( "ubiquitin-like hydrolase activity") -AnnotationAssertion( "ubiquitin-like protein-specific isopeptidase activity") -AnnotationAssertion( "ubiquitin-like protein-specific protease activity") -AnnotationAssertion( "ubiquitinyl-like hydrolase activity") -AnnotationAssertion( "ubiquitin-like specific protease activity") -AnnotationAssertion( "ubiquitin-like-protein-specific protease activity") -AnnotationAssertion( "ubiquitin-specific protease activity involved in negative regulation of ERAD pathway") -AnnotationAssertion( "ubiquitin-specific protease activity involved in positive regulation of ERAD pathway") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0019783") -AnnotationAssertion(rdfs:comment "While ubiquitin-like proteins can be rarely linked to substrates via bonds other than isopeptide bonds, all known ubiquitin-like peptidases cleave the isopeptide bond.") -AnnotationAssertion(rdfs:label "ubiquitin-like protein peptidase activity") -SubClassOf( ) - -# Class: (Atg8-specific peptidase activity) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:28901328") "A thiol-dependent isopeptidase activity that cleaves APG8 from a target protein to which it is conjugated.") -AnnotationAssertion( "Atg8-specific protease activity") +# Class: (protein-phosphatidylethanolamide deconjugating activity) + +AnnotationAssertion(Annotation( "PMID:22240591") Annotation( "PMID:22652539") Annotation( "PMID:28330855") Annotation( "PMID:2882172") Annotation( "PMID:28901328") "Catalysis of the reaction: [protein]-C-terminal L-amino acid-glycyl-phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine. An example of this reaction is the removal of ATG8 from membranes to which it is covalently linked to a phosphatidylethanolamid via its terminal glycine residue.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25472"^^xsd:anyURI) +AnnotationAssertion(Annotation( "skos:narrowMatch") "Atg8-specific protease activity") +AnnotationAssertion(Annotation( "GOC:vw") "APG8-specific protease activity") +AnnotationAssertion(Annotation( "skos:narrowMatch") "ATG8-PE deconjugation activity") +AnnotationAssertion(Annotation( "skos:narrowMatch") "ATG8-PE hydrolase activity") +AnnotationAssertion(Annotation( "skos:narrowMatch") "Atg8-specific peptidase activity") AnnotationAssertion( "molecular_function") -AnnotationAssertion( "APG8-PE hydrolase") -AnnotationAssertion(Annotation( "GOC:vw") "APG8-specific protease activity") +AnnotationAssertion(Annotation( "skos:narrowMatch") "APG8-PE hydrolase") AnnotationAssertion( "GO:0019786") -AnnotationAssertion(rdfs:label "Atg8-specific peptidase activity") -SubClassOf( ) -SubClassOf( ) +AnnotationAssertion(rdfs:label "protein-phosphatidylethanolamide deconjugating activity") +SubClassOf( ) +SubClassOf( ) # Class: (ubiquitin-like protein transferase activity) -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:rn") Annotation( "PMID:10806345") Annotation( "PMID:10884686") "Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y --> Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein.") +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:rn") Annotation( "PMID:10806345") Annotation( "PMID:10884686") "Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y = Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24697"^^xsd:anyURI) AnnotationAssertion( "GO:0008639") AnnotationAssertion( "GO:0008640") +AnnotationAssertion( "E2") AnnotationAssertion(Annotation(rdfs:label "ATG16L1 complex transfers LC3 from ATG3 to PE") "Reactome:R-HSA-5678490") AnnotationAssertion(Annotation(rdfs:label "RIP2 is K63 polyubiquitinated") "Reactome:R-HSA-688137") AnnotationAssertion(Annotation( "GOC:dph") "small conjugating protein transferase activity") @@ -40546,7 +40647,6 @@ AnnotationAssertion( "ubiquitin-like conjugating enzyme activity") AnnotationAssertion( "ubiquitin-like-protein ligase activity") AnnotationAssertion( "molecular_function") -AnnotationAssertion( "E2") AnnotationAssertion(Annotation( "GOC:dph") "E3") AnnotationAssertion( "GO:0019787") AnnotationAssertion( ) @@ -43052,8 +43152,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reproductive process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (digestive system process) @@ -43073,8 +43171,6 @@ AnnotationAssertion( "menstrual cycle process") AnnotationAssertion( "GO:0022602") AnnotationAssertion(rdfs:label "ovulation cycle process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43313,7 +43409,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -46561,7 +46657,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "nuclease regulator activity") AnnotationAssertion( "GO:0032069") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of nuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -46573,7 +46669,7 @@ AnnotationAssertion( "DNase regulator") AnnotationAssertion( "deoxyribonuclease regulator") AnnotationAssertion( "GO:0032070") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of deoxyribonuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -46588,7 +46684,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "nuclease inhibitor") AnnotationAssertion( "GO:0032074") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of nuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -46604,7 +46700,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "nuclease activator") AnnotationAssertion( "GO:0032075") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of nuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -46620,7 +46716,7 @@ AnnotationAssertion( "DNase inhibitor") AnnotationAssertion( "deoxyribonuclease inhibitor") AnnotationAssertion( "GO:0032076") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of deoxyribonuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -46637,7 +46733,7 @@ AnnotationAssertion( "DNase activator") AnnotationAssertion( "deoxyribonuclease activator") AnnotationAssertion( "GO:0032077") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of deoxyribonuclease activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -46651,7 +46747,7 @@ AnnotationAssertion( "inhibition of protein binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032091") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of protein binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -46665,7 +46761,7 @@ AnnotationAssertion( "stimulation of protein binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032092") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of protein binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -46990,6 +47086,7 @@ SubClassOf(Annotation( (myelin assembly) AnnotationAssertion(Annotation( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which the wraps of cell membrane that constitute myelin are laid down around an axon in the central or peripheral nervous system.") +AnnotationAssertion( "myelin sheath assembly") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "myelin formation") AnnotationAssertion( "GO:0032288") @@ -47001,6 +47098,7 @@ SubClassOf( ObjectSomeValuesFrom( (central nervous system myelin formation) AnnotationAssertion(Annotation( "GOC:dgh") "The process in which the wraps of cell membrane that constitute myelin are laid down around an axon by an oligodendrocyte in the central nervous system.") +AnnotationAssertion( "central nervous system myelin sheath formation") AnnotationAssertion( "myelin formation in central nervous system") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032289") @@ -47016,6 +47114,7 @@ SubClassOf( ObjectAllValuesFrom( "GOC:dgh") "The process in which the wraps of cell membrane that constitute myelin are laid down around an axon by Schwann cells in the peripheral nervous system.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19106"^^xsd:anyURI) AnnotationAssertion( "myelin formation in peripheral nervous system") +AnnotationAssertion( "peripheral nervous system myelin sheath formation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032290") AnnotationAssertion(rdfs:label "peripheral nervous system myelin formation") @@ -47451,7 +47550,7 @@ 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( ))) @@ -47464,7 +47563,7 @@ 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( ) @@ -47479,7 +47578,7 @@ 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( ) @@ -47491,7 +47590,7 @@ 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( ))) @@ -47505,7 +47604,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -47521,7 +47620,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -48779,7 +48878,7 @@ 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( ))) @@ -48796,7 +48895,7 @@ 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( ))) @@ -49611,14 +49710,13 @@ SubClassOf( (cellular component morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:tb") "The process in which cellular structures, including whole cells or cell parts, are generated and organized.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25496"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "cellular structure morphogenesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032989") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (cell part morphogenesis) @@ -50204,6 +50302,16 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (response to ATP) + +AnnotationAssertion(Annotation( "GOC:sl") "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 ATP (adenosine 5'-triphosphate) stimulus.") +AnnotationAssertion( "response to adenosine 5'-triphosphate") +AnnotationAssertion( "response to adenosine triphosphate") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0033198") +AnnotationAssertion(rdfs:label "response to ATP") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (iron import into cell) AnnotationAssertion(Annotation( "PMID:18622392") Annotation( "PMID:23192658") Annotation( "Wikipedia:Human_iron_metabolism") "The directed movement of iron ions from outside of a cell into the cytoplasmic compartment. This may occur via transport across the plasma membrane or via endocytosis.") @@ -50340,7 +50448,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mah") "Any process that modulates the frequency, rate or extent of collagen binding.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033341") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of collagen binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -50353,7 +50461,7 @@ AnnotationAssertion( "inhibition of collagen binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033342") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of collagen binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -50367,7 +50475,7 @@ AnnotationAssertion( "stimulation of collagen binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033343") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of collagen binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -50592,7 +50700,7 @@ AnnotationAssertion( "kinase inhibitor") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033673") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -50607,7 +50715,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -52181,7 +52289,7 @@ AnnotationAssertion( "2010-05-19T10:28:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035561") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of chromatin binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -52192,7 +52300,7 @@ AnnotationAssertion( "2010-05-19T10:29:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035562") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of chromatin binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -52203,7 +52311,7 @@ AnnotationAssertion( "2010-05-19T10:29:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035563") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of chromatin binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -54862,7 +54970,6 @@ AnnotationAssertion(rdfs:label "natu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (regulation of natural killer cell mediated cytotoxicity) @@ -56427,8 +56534,8 @@ 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( ))) @@ -56448,7 +56555,7 @@ 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( ))) @@ -57586,7 +57693,7 @@ AnnotationAssertion( "stimulation of DNA binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043388") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of DNA binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -57599,7 +57706,7 @@ AnnotationAssertion( "inhibition of DNA binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043392") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of DNA binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -57608,7 +57715,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of protein binding.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043393") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of protein binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -57739,7 +57846,7 @@ AnnotationAssertion( "regulation of adenosinetriphosphatase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043462") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of ATP-dependent activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -57849,6 +57956,16 @@ AnnotationAssertion( "positive regulation of neuron apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (ADP binding) + +AnnotationAssertion(Annotation( "GOC:jl") "Binding to ADP, adenosine 5'-diphosphate.") +AnnotationAssertion( "adenosine 5'-diphosphate binding") +AnnotationAssertion( "adenosine diphosphate binding") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0043531") +AnnotationAssertion(rdfs:label "ADP binding") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (blood vessel endothelial cell migration) AnnotationAssertion(Annotation( "PMID:11166264") "The orderly movement of an endothelial cell into the extracellular matrix in order to form new blood vessels during angiogenesis.") @@ -57904,7 +58021,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -58361,7 +58478,7 @@ AnnotationAssertion( "2009-04-21T04:07:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044092") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of molecular function") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -58373,7 +58490,7 @@ 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( ) @@ -58710,16 +58827,16 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) -# Class: (autophagy of nucleus) +# Class: (nucleophagy) AnnotationAssertion(Annotation( "GOC:autophagy") Annotation( "GOC:jl") Annotation( "PMID:24013549") "A form of autophagy, by which damaged or non-essential parts of the nucleus, or even an entire nucleus is degraded.") AnnotationAssertion( "jl") AnnotationAssertion( "2013-09-10T15:50:25Z") -AnnotationAssertion( "nucleus degradation") +AnnotationAssertion( "autophagy of nucleus") AnnotationAssertion( "biological_process") -AnnotationAssertion( "nucleophagy") +AnnotationAssertion( "nucleus degradation") AnnotationAssertion( "GO:0044804") -AnnotationAssertion(rdfs:label "autophagy of nucleus") +AnnotationAssertion(rdfs:label "nucleophagy") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -58806,6 +58923,16 @@ AnnotationAssertion(rdfs:label "plas EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (G protein-coupled ATP receptor activity) + +AnnotationAssertion(Annotation( "GOC:mah") "Combining with ATP and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.") +AnnotationAssertion( "ATP-activated nucleotide receptor activity") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "ATP-activated adenosine receptor activity") +AnnotationAssertion( "GO:0045031") +AnnotationAssertion(rdfs:label "G protein-coupled ATP receptor activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulated exocytosis) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0716731363") "A process of exocytosis in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand.") @@ -61705,7 +61832,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -61719,7 +61846,7 @@ 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( ) @@ -62529,6 +62656,35 @@ AnnotationAssertion( "negative regulation of T cell homeostatic proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (ADP metabolic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate.") +AnnotationAssertion( "ADP metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046031") +AnnotationAssertion(rdfs:label "ADP metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (ADP catabolic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways resulting in the breakdown of ADP, adenosine 5'-diphosphate.") +AnnotationAssertion( "ADP breakdown") +AnnotationAssertion( "ADP catabolism") +AnnotationAssertion( "ADP degradation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046032") +AnnotationAssertion(rdfs:label "ADP catabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (ATP metabolic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.") +AnnotationAssertion( "ATP metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046034") +AnnotationAssertion(rdfs:label "ATP metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (aldehyde biosynthetic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the formation of aldehydes, any organic compound with the formula R-CH=O.") @@ -65945,11 +66101,15 @@ EquivalentClasses( ObjectIntersection # Class: (stem cell differentiation) AnnotationAssertion(Annotation( "CL:0000034") Annotation( "GOC:isa_complete") "The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.") +AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Stem_cell_differentiation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048863") AnnotationAssertion(rdfs:label "stem cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (stem cell development) @@ -66463,6 +66623,11 @@ AnnotationAssertion( "[tyrosine 3-monooxygenase] kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (catecholamine secretion) @@ -67027,8 +67192,8 @@ AnnotationAssertion( "regulation of metalloenzyme activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050790") +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -68515,7 +68680,7 @@ SubClassOf( "GOC:ai") "Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051098") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -68529,7 +68694,7 @@ AnnotationAssertion( "stimulation of binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051099") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -68542,7 +68707,7 @@ AnnotationAssertion( "inhibition of binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051100") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -68551,7 +68716,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051101") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of DNA binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69344,7 +69509,7 @@ AnnotationAssertion(Annotation( "hydrolase regulator") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051336") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of hydrolase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69354,8 +69519,8 @@ AnnotationAssertion(Annotation( "transferase regulator") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051338") +AnnotationAssertion( ) 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( ))) @@ -69366,7 +69531,7 @@ AnnotationAssertion(Annotation( "ligase regulator") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051340") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of ligase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69381,7 +69546,7 @@ AnnotationAssertion( "stimulation of hydrolase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051345") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of hydrolase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69395,7 +69560,7 @@ AnnotationAssertion( "inhibition of hydrolase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051346") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of hydrolase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69410,8 +69575,8 @@ AnnotationAssertion( "stimulation of transferase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051347") +AnnotationAssertion( ) 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( ))) @@ -69426,8 +69591,8 @@ AnnotationAssertion( "inhibition of transferase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051348") +AnnotationAssertion( ) 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( ))) @@ -69443,7 +69608,7 @@ AnnotationAssertion( "stimulation of ligase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051351") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of ligase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -69457,7 +69622,7 @@ AnnotationAssertion( "inhibition of ligase activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051352") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of ligase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -70897,17 +71062,6 @@ AnnotationAssertion( "negative regulation of chromosome segregation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of peptidase activity) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "peptidase regulator activity") -AnnotationAssertion( "GO:0052547") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of peptidase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) - # Class: (imidazole-containing compound metabolic process) AnnotationAssertion(Annotation( "GOC:curators") "The chemical reactions and pathways involving imidazoles, five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton.") @@ -76100,7 +76254,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -76112,7 +76266,7 @@ 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( ) @@ -76124,7 +76278,7 @@ 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( ) @@ -78381,23 +78535,23 @@ SubClassOf( (ubiquitin-like protein conjugating enzyme activity) -AnnotationAssertion(Annotation( "GOC:dph") "Isoenergetic transfer of a ubiquitin-like protein (ULP) from one protein to another via the reaction X-SCP + Y -> Y-SCP + X, where both the X-SCP and Y-SCP linkages are thioester bonds between the C-terminal amino acid of SCP and a sulfhydryl side group of a cysteine residue.") +AnnotationAssertion(Annotation( "GOC:dph") "Isoenergetic transfer of a ubiquitin-like protein (ULP) from one protein to another via the reaction X-SCP + Y = Y-SCP + X, where both the X-SCP and Y-SCP linkages are thioester bonds between the C-terminal amino acid of SCP and a sulfhydryl side group of a cysteine residue.") AnnotationAssertion( "dph") AnnotationAssertion( "2014-11-06T13:15:27Z") +AnnotationAssertion( "E2") AnnotationAssertion(Annotation( "GOC:dph") "small conjugating protein conjugating enzyme activity") AnnotationAssertion( "molecular_function") -AnnotationAssertion( "E2") AnnotationAssertion( "GO:0061650") AnnotationAssertion(rdfs:label "ubiquitin-like protein conjugating enzyme activity") SubClassOf( ) # Class: (Atg12 conjugating enzyme activity) -AnnotationAssertion(Annotation( "GOC:dph") "Isoenergetic transfer of Atg12 from one protein to another via the reaction X-Atg12 + Y -> Y-Atg12 + X, where both the X-Atg12 and Y-Atg12 linkages are thioester bonds between the C-terminal amino acid of Atg12 and a sulfhydryl side group of a cysteine residue.") +AnnotationAssertion(Annotation( "GOC:dph") "Isoenergetic transfer of Atg12 from one protein to another via the reaction X-Atg12 + Y = Y-Atg12 + X, where both the X-Atg12 and Y-Atg12 linkages are thioester bonds between the C-terminal amino acid of Atg12 and a sulfhydryl side group of a cysteine residue.") AnnotationAssertion( "dph") AnnotationAssertion( "2014-11-06T13:17:36Z") +AnnotationAssertion(Annotation( "GOC:dph") "E2") AnnotationAssertion( "molecular_function") -AnnotationAssertion(Annotation( "GOC:dph") "E2") AnnotationAssertion( "GO:0061651") AnnotationAssertion(rdfs:label "Atg12 conjugating enzyme activity") SubClassOf( ) @@ -78405,7 +78559,7 @@ SubClassOf( (ubiquitin-like protein ligase activity) -AnnotationAssertion(Annotation( "GOC:dph") "Catalysis of the transfer of a ubiquitin-like protein (ULP) to a substrate protein via the reaction X-ULP + S --> X + S-ULP, where X is either an E2 or E3 enzyme, the X-ULP linkage is a thioester bond, and the S-ULP linkage is an isopeptide bond between the C-terminal glycine of ULP and the epsilon-amino group of lysine residues in the substrate.") +AnnotationAssertion(Annotation( "GOC:dph") "Catalysis of the transfer of a ubiquitin-like protein (ULP) to a substrate protein via the reaction X-ULP + S = X + S-ULP, where X is either an E2 or E3 enzyme, the X-ULP linkage is a thioester bond, and the S-ULP linkage is an isopeptide bond between the C-terminal glycine of ULP and the epsilon-amino group of lysine residues in the substrate.") AnnotationAssertion( "dph") AnnotationAssertion( "2014-11-06T13:46:23Z") AnnotationAssertion(Annotation( "GOC:dph") "small conjugating protein ligase activity") @@ -78418,11 +78572,11 @@ SubClassOf( (Atg12 ligase activity) -AnnotationAssertion(Annotation( "GOC:dph") "Catalysis of the transfer of Atg12 to a substrate protein via the reaction X-Atg12 + S --> X + S-Atg12, where X is either an E2 or E3 enzyme, the X-Atg12 linkage is a thioester bond, and the S-Atg12 linkage is an isopeptide bond between the C-terminal amino acid of Atg12 and the epsilon-amino group of lysine residues in the substrate.") +AnnotationAssertion(Annotation( "GOC:dph") "Catalysis of the transfer of Atg12 to a substrate protein via the reaction X-Atg12 + S = X + S-Atg12, where X is either an E2 or E3 enzyme, the X-Atg12 linkage is a thioester bond, and the S-Atg12 linkage is an isopeptide bond between the C-terminal amino acid of Atg12 and the epsilon-amino group of lysine residues in the substrate.") AnnotationAssertion( "dph") AnnotationAssertion( "2014-11-06T13:50:42Z") +AnnotationAssertion(Annotation( "GOC:dph") "E3") AnnotationAssertion( "molecular_function") -AnnotationAssertion(Annotation( "GOC:dph") "E3") AnnotationAssertion( "GO:0061660") AnnotationAssertion(rdfs:label "Atg12 ligase activity") SubClassOf( ) @@ -78492,7 +78646,7 @@ SubClassOf( (secretory granule maturation) -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "GOC:dph") Annotation( "PMID:16618809") "Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodelling.") +AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "GOC:dph") Annotation( "PMID:16618809") "Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodeling.") AnnotationAssertion( "dph") AnnotationAssertion( "2016-09-09T13:24:34Z") AnnotationAssertion( "biological_process") @@ -78771,7 +78925,6 @@ AnnotationAssertion( "GO:0062014") AnnotationAssertion(rdfs:label "negative regulation of small molecule metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (collagen-containing extracellular matrix) @@ -78985,7 +79138,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of molecular function") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -80398,6 +80550,18 @@ AnnotationAssertion(rdfs:label "cell SubClassOf( ) SubClassOf( ) +# Class: (cellular response to ATP) + +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 ATP (adenosine 5'-triphosphate) stimulus.") +AnnotationAssertion( "mah") +AnnotationAssertion( "2009-12-10T05:09:47Z") +AnnotationAssertion(Annotation( "GOC:mah") "cellular response to adenosine 5'-triphosphate") +AnnotationAssertion(Annotation( "GOC:mah") "cellular response to adenosine triphosphate") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0071318") +AnnotationAssertion(rdfs:label "cellular response to ATP") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (cellular response to carbohydrate 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 a carbohydrate stimulus.") @@ -81445,7 +81609,7 @@ AnnotationAssertion( "2010-09-15T03:08:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071900") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of protein serine/threonine kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -81456,7 +81620,7 @@ AnnotationAssertion( "2010-09-15T03:09:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071901") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of protein serine/threonine kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -81467,7 +81631,7 @@ AnnotationAssertion( "2010-09-15T03:09:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071902") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of protein serine/threonine kinase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -87578,8 +87742,8 @@ 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 funtion 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( ))) SubClassOf( ) @@ -88430,8 +88594,8 @@ 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 funtion 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( ))) @@ -88969,7 +89133,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -88981,7 +89145,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -88993,7 +89157,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -90798,7 +90962,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of receptor ligand") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900120") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of receptor binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -90815,7 +90979,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of receptor-associated protein activity") AnnotationAssertion( "GO:1900121") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of receptor binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -90829,7 +90993,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of receptor binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900122") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of receptor binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -90925,7 +91089,7 @@ AnnotationAssertion( "2012-02-23T04:05:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900130") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of lipid binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -90940,7 +91104,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of lipid binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900131") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of lipid binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -90955,7 +91119,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of lipid binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900132") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of lipid binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -91886,7 +92050,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -91902,7 +92066,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -91918,7 +92082,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -93730,7 +93894,7 @@ AnnotationAssertion( AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of calcium ion storage activity") AnnotationAssertion( "GO:1901876") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of calcium ion binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -93750,7 +93914,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of calcium ion storage activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of calcium ion storage activity") AnnotationAssertion( "GO:1901877") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of calcium ion binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -93770,7 +93934,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of calcium ion storage activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of calcium ion storage activity") AnnotationAssertion( "GO:1901878") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of calcium ion binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -94778,7 +94942,7 @@ 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( ))) @@ -94798,7 +94962,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of aquaporin") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902428") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of water channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -94820,7 +94984,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -96857,7 +97021,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -96873,7 +97037,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of acetylcholine-gated cation channel activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903049") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of acetylcholine-gated cation channel activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -98506,6 +98670,55 @@ AnnotationAssertion( "positive regulation of protein localization to ciliary membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of ATP metabolic process) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20695849") "Any process that modulates the frequency, rate or extent of ATP metabolic process.") +AnnotationAssertion( "sl") +AnnotationAssertion( "2014-10-30T19:04:24Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATP metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1903578") +AnnotationAssertion(rdfs:label "regulation of ATP metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of ATP metabolic process) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20695849") "Any process that stops, prevents or reduces the frequency, rate or extent of ATP metabolic process.") +AnnotationAssertion( "sl") +AnnotationAssertion( "2014-10-30T19:04:33Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATP metabolic process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATP metabolism") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATP metabolic process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATP metabolism") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATP metabolic process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATP metabolism") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATP metabolism") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATP metabolic process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATP metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1903579") +AnnotationAssertion(rdfs:label "negative regulation of ATP metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of ATP metabolic process) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20695849") "Any process that activates or increases the frequency, rate or extent of ATP metabolic process.") +AnnotationAssertion( "sl") +AnnotationAssertion( "2014-10-30T19:04:42Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATP metabolism") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATP metabolic process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATP metabolism") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATP metabolic process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATP metabolism") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATP metabolic process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATP metabolism") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATP metabolic process") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATP metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1903580") +AnnotationAssertion(rdfs:label "positive regulation of ATP metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of basophil degranulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10880837") "Any process that modulates the frequency, rate or extent of basophil degranulation.") @@ -100600,7 +100813,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -100627,7 +100840,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -100655,7 +100868,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of iron-specific channel activity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904256") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of iron ion transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -101591,7 +101804,7 @@ AnnotationAssertion( "GOC:TermGenie") "regulation of microtubule severing activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of microtubule/chromatin interaction") AnnotationAssertion( "GO:1904526") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of microtubule binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -101616,7 +101829,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of microtubule severing activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of microtubule/chromatin interaction") AnnotationAssertion( "GO:1904527") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of microtubule binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -101641,7 +101854,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of microtubule severing activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of microtubule/chromatin interaction") AnnotationAssertion( "GO:1904528") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of microtubule binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -103026,7 +103239,7 @@ AnnotationAssertion( "2015-11-09T11:43:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904793") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of euchromatin binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -103041,7 +103254,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of euchromatin binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904794") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of euchromatin binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -103056,7 +103269,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of euchromatin binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904795") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of euchromatin binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -104497,7 +104710,7 @@ AnnotationAssertion( "2016-06-06T10:20:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905214") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of RNA binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -104512,7 +104725,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of RNA binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905215") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of RNA binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -104527,7 +104740,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of RNA binding") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905216") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of RNA binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -105112,19 +105325,6 @@ AnnotationAssertion( "pericyte cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (peptidase complex) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000088") Annotation( "PMID:1689240") "A protein complex which is capable of peptidase activity.") -AnnotationAssertion( "bhm") -AnnotationAssertion( "2016-08-16T12:49:36Z") -AnnotationAssertion( "protease complex") -AnnotationAssertion( "tryptase complex") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:1905368") -AnnotationAssertion(rdfs:comment "An example of this is PLAU in human (UniProt symbol P00749) in PMID:1689240 (inferred from direct assay).") -AnnotationAssertion(rdfs:label "peptidase complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (protein localization to presynapse) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:24449494") "A process in which a protein is transported to, or maintained in, a location within a presynapse.") @@ -109132,7 +109332,7 @@ 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( ) @@ -109146,7 +109346,7 @@ 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( ) @@ -111888,6 +112088,51 @@ SubClassOf( ) SubClassOf( ) +# Class: (regulation of ATP biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of ATP biosynthetic process.") +AnnotationAssertion( "kmv") +AnnotationAssertion( "2011-10-26T03:18:03Z") +AnnotationAssertion(Annotation( "GOC:obol") "regulation of ATP anabolism") +AnnotationAssertion(Annotation( "GOC:obol") "regulation of ATP biosynthesis") +AnnotationAssertion(Annotation( "GOC:obol") "regulation of ATP formation") +AnnotationAssertion(Annotation( "GOC:obol") "regulation of ATP synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:obol") "regulation of ATP regeneration") +AnnotationAssertion( "GO:2001169") +AnnotationAssertion(rdfs:label "regulation of ATP biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of ATP biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of ATP biosynthetic process.") +AnnotationAssertion( "kmv") +AnnotationAssertion( "2011-10-26T03:18:13Z") +AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of ATP anabolism") +AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of ATP biosynthesis") +AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of ATP formation") +AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of ATP synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of ATP regeneration") +AnnotationAssertion( "GO:2001170") +AnnotationAssertion(rdfs:label "negative regulation of ATP biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of ATP biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of ATP biosynthetic process.") +AnnotationAssertion( "kmv") +AnnotationAssertion( "2011-10-26T03:18:26Z") +AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ATP anabolism") +AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ATP biosynthesis") +AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ATP formation") +AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ATP synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ATP regeneration") +AnnotationAssertion( "GO:2001171") +AnnotationAssertion(rdfs:label "positive regulation of ATP biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of CD8-positive, alpha-beta T cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of CD8-positive, alpha-beta T cell activation.") @@ -112175,7 +112420,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -112189,7 +112434,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -112203,7 +112448,7 @@ 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(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) @@ -115889,7 +116134,6 @@ AnnotationAssertion( "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].") AnnotationAssertion(rdfs:label "protein") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -116072,7 +116316,7 @@ SubClassOf( (CD3 subunit with immunoglobulin domain) -AnnotationAssertion(Annotation( "PMID:16473826") Annotation( "PMID:1724736") "A protein that has a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.") +AnnotationAssertion(Annotation( "PMID:16473826") Annotation( "PMID:1724736") "A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.") AnnotationAssertion( "PIRSF:PIRSF001993") AnnotationAssertion( "CD3 subunit with Ig-like domain") AnnotationAssertion( "protein") @@ -116181,6 +116425,7 @@ SubClassOf( (T-cell surface glycoprotein CD8 alpha chain) AnnotationAssertion(Annotation( "PMID:11114424") Annotation( "PRO:CNA") Annotation( "Wikipedia:CD8") "A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain.") +AnnotationAssertion( "PANTHER:PTHR10441:SF1") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CD8A") AnnotationAssertion( "CD8a") AnnotationAssertion( "T-cell surface glycoprotein Lyt-2") @@ -116512,6 +116757,7 @@ SubClassOf( "PMID:12037138") Annotation( "PRO:WCB") "A chemokine receptor that is a translation product of the human CXCR5 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL13.") AnnotationAssertion( "IUPHARobj:72") +AnnotationAssertion( "PANTHER:PTHR24227:SF213") AnnotationAssertion( "CD185") AnnotationAssertion( "CXC-R5") AnnotationAssertion( "CXCR-5") @@ -116818,6 +117064,7 @@ SubClassOf( (CD48 molecule) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof.") +AnnotationAssertion( "PANTHER:PTHR12080:SF3") AnnotationAssertion( "PIRSF:PIRSF001973") AnnotationAssertion( "B-lymphocyte activation marker BLAST-1") AnnotationAssertion( "BCM1 surface antigen") @@ -116884,6 +117131,7 @@ SubClassOf( (SLAM family member 5) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human CD84 gene or a 1:1 ortholog thereof.") +AnnotationAssertion( "PANTHER:PTHR12080:SF6") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CD84") AnnotationAssertion( "cell surface antigen MAX.3") AnnotationAssertion( "hly9-beta") @@ -117178,6 +117426,7 @@ SubClassOf( "PRO:WCB") "A B7-related protein that is a translation product of the human CD86 gene or a 1:1 ortholog thereof.") AnnotationAssertion( "IUPHARobj:2745") +AnnotationAssertion( "PANTHER:PTHR25462:SF45") AnnotationAssertion( "B70") AnnotationAssertion( "BU63") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CD86") @@ -117422,6 +117671,7 @@ SubClassOf( "PRO:WCB") "A vasopressin/oxytocin receptor that is a translation product of the human OXTR gene or a 1:1 ortholog thereof. The preferred ligand is oxytocin.") AnnotationAssertion( "IUPHARobj:369") +AnnotationAssertion( "PANTHER:PTHR24241:SF46") AnnotationAssertion( "OT-R") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "OXTR") AnnotationAssertion( "protein") @@ -117432,7 +117682,7 @@ SubClassOf( (transcription factor NF-kappa-B subunit) -AnnotationAssertion(Annotation( "PRO:JAN") "A protein that has a core domain composition consisting of a Rel homology domain (RHD) (Pfam:PF00554), an IPT/TIG domain (Pfam:PF01833), six copies of the Ankyrin repeat (Pfam:PF00023), a Death domain (Pfam:PF00531) and a C-terminal PEST region.") +AnnotationAssertion(Annotation( "PRO:JAN") "A protein with a core domain composition consisting of a Rel homology domain (RHD) (Pfam:PF00554), an IPT/TIG domain (Pfam:PF01833), six copies of the Ankyrin repeat (Pfam:PF00023), a Death domain (Pfam:PF00531) and a C-terminal PEST region.") AnnotationAssertion( "PIRSF:PIRSF036310") AnnotationAssertion( "protein") AnnotationAssertion( "transcription factor NF-kappa-B") @@ -117571,6 +117821,7 @@ SubClassOf( (SLAM family member 1) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof.") +AnnotationAssertion( "PANTHER:PTHR12080:SF1") AnnotationAssertion( "CD150") AnnotationAssertion( "CDw150") AnnotationAssertion( "IPO-3") @@ -117627,6 +117878,7 @@ SubClassOf( (T-cell surface glycoprotein CD5) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof.") +AnnotationAssertion( "PANTHER:PTHR19331:SF6") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CD5") AnnotationAssertion( "Lyt-1") AnnotationAssertion( "ly-1") @@ -118524,6 +118776,7 @@ SubClassOf( "PRO:WCB") "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human PDGFRA gene or a 1:1 ortholog thereof.") AnnotationAssertion( "IUPHARobj:1803") +AnnotationAssertion( "PANTHER:PTHR24416:SF207") AnnotationAssertion( "PIRSF:PIRSF500950") AnnotationAssertion( "CD140 antigen-like family member A") AnnotationAssertion( "CD140a") @@ -119813,8 +120066,6 @@ SubClassOf( "PRO:DNx") "A protein that is a translation product of the human SCGB1A1 gene or a 1:1 ortholog thereof.") AnnotationAssertion( "CCPBP") -AnnotationAssertion( "Club cell phospholipid-binding protein") -AnnotationAssertion( "Club cells 10 kDa secretory protein") AnnotationAssertion( "PCB-binding protein") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "SCGB1A1") AnnotationAssertion( "UP-1") @@ -119995,10 +120246,10 @@ AnnotationAssertion(Annotation( "PRO:DAN") "polypeptide") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000018263") -AnnotationAssertion(rdfs:comment "Category=polymer.") +AnnotationAssertion(rdfs:comment "Category=external.") AnnotationAssertion(rdfs:label "amino acid chain") SubClassOf( ) -SubClassOf( ObjectMinCardinality(2 )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (proteolytic cleavage product) @@ -120865,21 +121116,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (protein-containing material entity) - -AnnotationAssertion(Annotation( "PRO:DAN") "A material entity that minimally consists of a protein.") -AnnotationAssertion(Annotation( "PRO:DAN") "protein") -AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") -AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") -AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") -AnnotationAssertion( "protein") -AnnotationAssertion( "PR:000050567") -AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).") -AnnotationAssertion(rdfs:label "protein-containing material entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (SCO-spondin (human)) AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:A2VEC9") "A SCO-spondin that is encoded in the genome of human.") @@ -123014,10 +123250,10 @@ SubClassOf( ObjectSomeValuesFrom( "PRO:DNx") Annotation( "UniProtKB:P11684") "A uteroglobin that is encoded in the genome of human.") AnnotationAssertion( "UniProtKB:P11684") AnnotationAssertion(Annotation( "UniProtKB:P11684") "CCPBP (human)") -AnnotationAssertion(Annotation( "UniProtKB:P11684") "Club cell phospholipid-binding protein (human)") -AnnotationAssertion(Annotation( "UniProtKB:P11684") "Club cells 10 kDa secretory protein (human)") AnnotationAssertion(Annotation( "UniProtKB:P11684") "UP-1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P11684") "UP1 (human)") +AnnotationAssertion(Annotation( "UniProtKB:P11684") "clara cell phospholipid-binding protein (human)") +AnnotationAssertion(Annotation( "UniProtKB:P11684") "clara cells 10 kDa secretory protein (human)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hSCGB1A1") AnnotationAssertion(Annotation( "UniProtKB:P11684") "secretoglobin family 1A member 1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P11684") "urinary protein 1 (human)") @@ -126996,10 +127232,10 @@ AnnotationAssertion(Annotation( "UniProtKB:Q06318") AnnotationAssertion(Annotation( "UniProtKB:Q06318") "CC10 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:Q06318") "CCPBP (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:Q06318") "Club cell 17 kDa protein (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:Q06318") "Club cell phospholipid-binding protein (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:Q06318") "Club cells 10 kDa secretory protein (mouse)") AnnotationAssertion(Annotation( "UniProtKB:Q06318") "PCB-binding protein (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q06318") "clara cell 17 kDa protein (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q06318") "clara cell phospholipid-binding protein (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q06318") "clara cells 10 kDa secretory protein (mouse)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mSCGB1A1") AnnotationAssertion(Annotation( "UniProtKB:Q06318") "secretoglobin family 1A member 1 (mouse)") AnnotationAssertion( "protein") diff --git a/src/ontology/imports/pr_terms.txt b/src/ontology/imports/pr_terms.txt index b91fa3bec..aa4ed3624 100644 --- a/src/ontology/imports/pr_terms.txt +++ b/src/ontology/imports/pr_terms.txt @@ -5,6 +5,7 @@ PR:000001175 PR:000001177 PR:000001635 PR:000002030 +PR:000002123 PR:000003264 PR:000004724 PR:000009344 diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 9ab5d7803..5fc4d25fa 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,9 +7,8 @@ Prefix(rdfs:=) Ontology( - - -Annotation(owl:versionInfo "2023-06-14") + +Annotation(owl:versionInfo "2023-06-16") From 979623f0fd164352b923cd6190f8ef2105a9108d Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 20 Jun 2023 11:13:56 +0100 Subject: [PATCH 5/5] Refresh imports --- src/ontology/imports/merged_import.owl | 170 ++++++++++++++++++++++--- src/patterns/definitions.owl | 4 +- 2 files changed, 151 insertions(+), 23 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 7c128191d..811a3d94b 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 "2023-06-16") + +Annotation(owl:versionInfo "2023-06-20") Declaration(Class()) Declaration(Class()) @@ -8275,6 +8275,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8333,6 +8334,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8348,6 +8350,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8453,6 +8456,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8508,6 +8512,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8602,6 +8607,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8609,6 +8615,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13832,6 +13839,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -14120,7 +14128,7 @@ AnnotationAssertion(rdfs:label "has AnnotationAssertion(rdfs:label "term replaced by") -# Annotation Property: (never_in_taxon) +# Annotation Property: (never in taxon) AnnotationAssertion( "tooth SubClassOf 'never in taxon' value 'Aves'") AnnotationAssertion(Annotation( "PMID:20973947") "S never_in_taxon T iff: S SubClassOf in_taxon only not T.") @@ -112740,6 +112748,8 @@ AnnotationAssertion( "PMID:12054223") AnnotationAssertion( "PMID:2112744") AnnotationAssertion( "PMID:270744") +AnnotationAssertion( "PMID:32628106") +AnnotationAssertion( "PMID:36748408") AnnotationAssertion( "PMID:7520741") AnnotationAssertion( "PMID:8123559") AnnotationAssertion( "PMID:8186100") @@ -112814,6 +112824,8 @@ AnnotationAssertion( "PMID:2112744") AnnotationAssertion( "PMID:25527841") AnnotationAssertion( "PMID:270744") +AnnotationAssertion( "PMID:32628106") +AnnotationAssertion( "PMID:36748408") AnnotationAssertion( "PMID:8123559") AnnotationAssertion( "PMID:8590690") AnnotationAssertion( "PMID:9103655") @@ -116134,6 +116146,7 @@ AnnotationAssertion( "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].") AnnotationAssertion(rdfs:label "protein") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -116316,7 +116329,7 @@ SubClassOf( (CD3 subunit with immunoglobulin domain) -AnnotationAssertion(Annotation( "PMID:16473826") Annotation( "PMID:1724736") "A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.") +AnnotationAssertion(Annotation( "PMID:16473826") Annotation( "PMID:1724736") "A protein that has a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.") AnnotationAssertion( "PIRSF:PIRSF001993") AnnotationAssertion( "CD3 subunit with Ig-like domain") AnnotationAssertion( "protein") @@ -116425,7 +116438,6 @@ SubClassOf( (T-cell surface glycoprotein CD8 alpha chain) AnnotationAssertion(Annotation( "PMID:11114424") Annotation( "PRO:CNA") Annotation( "Wikipedia:CD8") "A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain.") -AnnotationAssertion( "PANTHER:PTHR10441:SF1") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CD8A") AnnotationAssertion( "CD8a") AnnotationAssertion( "T-cell surface glycoprotein Lyt-2") @@ -116757,7 +116769,6 @@ SubClassOf( "PMID:12037138") Annotation( "PRO:WCB") "A chemokine receptor that is a translation product of the human CXCR5 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL13.") AnnotationAssertion( "IUPHARobj:72") -AnnotationAssertion( "PANTHER:PTHR24227:SF213") AnnotationAssertion( "CD185") AnnotationAssertion( "CXC-R5") AnnotationAssertion( "CXCR-5") @@ -117064,7 +117075,6 @@ SubClassOf( (CD48 molecule) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof.") -AnnotationAssertion( "PANTHER:PTHR12080:SF3") AnnotationAssertion( "PIRSF:PIRSF001973") AnnotationAssertion( "B-lymphocyte activation marker BLAST-1") AnnotationAssertion( "BCM1 surface antigen") @@ -117131,7 +117141,6 @@ SubClassOf( (SLAM family member 5) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human CD84 gene or a 1:1 ortholog thereof.") -AnnotationAssertion( "PANTHER:PTHR12080:SF6") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CD84") AnnotationAssertion( "cell surface antigen MAX.3") AnnotationAssertion( "hly9-beta") @@ -117426,7 +117435,6 @@ SubClassOf( "PRO:WCB") "A B7-related protein that is a translation product of the human CD86 gene or a 1:1 ortholog thereof.") AnnotationAssertion( "IUPHARobj:2745") -AnnotationAssertion( "PANTHER:PTHR25462:SF45") AnnotationAssertion( "B70") AnnotationAssertion( "BU63") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CD86") @@ -117671,7 +117679,6 @@ SubClassOf( "PRO:WCB") "A vasopressin/oxytocin receptor that is a translation product of the human OXTR gene or a 1:1 ortholog thereof. The preferred ligand is oxytocin.") AnnotationAssertion( "IUPHARobj:369") -AnnotationAssertion( "PANTHER:PTHR24241:SF46") AnnotationAssertion( "OT-R") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "OXTR") AnnotationAssertion( "protein") @@ -117682,7 +117689,7 @@ SubClassOf( (transcription factor NF-kappa-B subunit) -AnnotationAssertion(Annotation( "PRO:JAN") "A protein with a core domain composition consisting of a Rel homology domain (RHD) (Pfam:PF00554), an IPT/TIG domain (Pfam:PF01833), six copies of the Ankyrin repeat (Pfam:PF00023), a Death domain (Pfam:PF00531) and a C-terminal PEST region.") +AnnotationAssertion(Annotation( "PRO:JAN") "A protein that has a core domain composition consisting of a Rel homology domain (RHD) (Pfam:PF00554), an IPT/TIG domain (Pfam:PF01833), six copies of the Ankyrin repeat (Pfam:PF00023), a Death domain (Pfam:PF00531) and a C-terminal PEST region.") AnnotationAssertion( "PIRSF:PIRSF036310") AnnotationAssertion( "protein") AnnotationAssertion( "transcription factor NF-kappa-B") @@ -117758,6 +117765,17 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "C-type lectin domain family 7 member A") SubClassOf( ) +# Class: (C/C-C motif small inducible chemokine) + +AnnotationAssertion(Annotation( "PRO:WCB") "A protein with core architecture consisting of a Small cytokines (intecrine/chemokine), interleukin-8 like (Pfam:PF00048) domain.") +AnnotationAssertion( "PIRSF:PIRSF001950") +AnnotationAssertion(Annotation( "PRO:DAN") Annotation( ) "fam:C/C-C chemokine") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000001808") +AnnotationAssertion(rdfs:comment "Category=family.") +AnnotationAssertion(rdfs:label "C/C-C motif small inducible chemokine") +SubClassOf( ) + # Class: (CD59-like glycoprotein) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human CD59 gene, a 1:1 ortholog thereof, or pro-orthologs thereof.") @@ -117821,7 +117839,6 @@ SubClassOf( (SLAM family member 1) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof.") -AnnotationAssertion( "PANTHER:PTHR12080:SF1") AnnotationAssertion( "CD150") AnnotationAssertion( "CDw150") AnnotationAssertion( "IPO-3") @@ -117878,7 +117895,6 @@ SubClassOf( (T-cell surface glycoprotein CD5) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof.") -AnnotationAssertion( "PANTHER:PTHR19331:SF6") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CD5") AnnotationAssertion( "Lyt-1") AnnotationAssertion( "ly-1") @@ -118676,6 +118692,16 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "vascular endothelial growth factor receptor") SubClassOf( ) +# Class: (C-C motif chemokine 3/4) + +AnnotationAssertion(Annotation( "PRO:WCB") "A C/C-C motif small inducible chemokine that is a translation product of the CCL3, CCL3L1/CCL3L3, or CCL4 gene.") +AnnotationAssertion( "PIRSF:PIRSF500569") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000001998") +AnnotationAssertion(rdfs:comment "Category=family.") +AnnotationAssertion(rdfs:label "C-C motif chemokine 3/4") +SubClassOf( ) + # Class: (receptor-type tyrosine-protein kinase FLT3) AnnotationAssertion(Annotation( "PRO:WCB") "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human FLT3 gene or a 1:1 ortholog thereof.") @@ -118776,7 +118802,6 @@ SubClassOf( "PRO:WCB") "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human PDGFRA gene or a 1:1 ortholog thereof.") AnnotationAssertion( "IUPHARobj:1803") -AnnotationAssertion( "PANTHER:PTHR24416:SF207") AnnotationAssertion( "PIRSF:PIRSF500950") AnnotationAssertion( "CD140 antigen-like family member A") AnnotationAssertion( "CD140a") @@ -118943,6 +118968,30 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "vascular endothelial growth factor receptor 2") SubClassOf( ) +# Class: (C-C motif chemokine 3) + +AnnotationAssertion(Annotation( "PRO:WCB") "A C-C motif chemokine 3/4 that is a translation product of the human CCL3 gene or a 1:1 ortholog thereof.") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CCL3") +AnnotationAssertion( "G0/G1 switch regulatory protein 19-1") +AnnotationAssertion( "L2G25B") +AnnotationAssertion( "MIP-1-alpha") +AnnotationAssertion( "PAT 464.1") +AnnotationAssertion( "SIS-alpha") +AnnotationAssertion( "SIS-beta") +AnnotationAssertion( "TY-5") +AnnotationAssertion( "heparin-binding chemotaxis protein") +AnnotationAssertion( "macrophage inflammatory protein 1-alpha") +AnnotationAssertion( "small-inducible cytokine A3") +AnnotationAssertion( "tonsillar lymphocyte LD78 alpha protein") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( ) "G0S19-1") +AnnotationAssertion(Annotation( ) "MIP1A") +AnnotationAssertion(Annotation( ) "SCYA3") +AnnotationAssertion( "PR:000002123") +AnnotationAssertion(rdfs:comment "Category=gene.") +AnnotationAssertion(rdfs:label "C-C motif chemokine 3") +SubClassOf( ) + # Class: (macrophage mannose receptor 1) AnnotationAssertion(Annotation( "PMID:8297379") Annotation( "PRO:CNA") "A C-type lectin with multiple lectin domains that is a translation product of the human MRC1 gene or a 1:1 ortholog thereof.") @@ -120066,6 +120115,8 @@ SubClassOf( "PRO:DNx") "A protein that is a translation product of the human SCGB1A1 gene or a 1:1 ortholog thereof.") AnnotationAssertion( "CCPBP") +AnnotationAssertion( "Club cell phospholipid-binding protein") +AnnotationAssertion( "Club cells 10 kDa secretory protein") AnnotationAssertion( "PCB-binding protein") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "SCGB1A1") AnnotationAssertion( "UP-1") @@ -120246,10 +120297,10 @@ AnnotationAssertion(Annotation( "PRO:DAN") "polypeptide") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000018263") -AnnotationAssertion(rdfs:comment "Category=external.") +AnnotationAssertion(rdfs:comment "Category=polymer.") AnnotationAssertion(rdfs:label "amino acid chain") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectMinCardinality(2 )) # Class: (proteolytic cleavage product) @@ -120440,6 +120491,19 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (C-C motif chemokine 3 proteolytic cleavage product) + +AnnotationAssertion(Annotation( "PRO:DNx") "A C-C motif chemokine 3 that has been processed by proteolytic cleavage.") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CCL3/ClvPrd") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000018732") +AnnotationAssertion(rdfs:comment "Category=modification.") +AnnotationAssertion(rdfs:label "C-C motif chemokine 3 proteolytic cleavage product") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (collagen alpha-1(I) chain proteolytic cleavage product) AnnotationAssertion(Annotation( "PRO:DNx") "A collagen alpha-1(I) chain that has been processed by proteolytic cleavage.") @@ -121116,6 +121180,21 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing material entity) + +AnnotationAssertion(Annotation( "PRO:DAN") "A material entity that minimally consists of a protein.") +AnnotationAssertion(Annotation( "PRO:DAN") "protein") +AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") +AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") +AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000050567") +AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).") +AnnotationAssertion(rdfs:label "protein-containing material entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (SCO-spondin (human)) AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:A2VEC9") "A SCO-spondin that is encoded in the genome of human.") @@ -122940,6 +123019,31 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (C-C motif chemokine 3 (human)) + +AnnotationAssertion(Annotation( "PRO:WCB") Annotation( "UniProtKB:P10147") "A C-C motif chemokine 3 that is encoded in the genome of human.") +AnnotationAssertion( "UniProtKB:P10147") +AnnotationAssertion(Annotation( "UniProtKB:P10147") "G0/G1 switch regulatory protein 19-1 (human)") +AnnotationAssertion(Annotation( "UniProtKB:P10147") "MIP-1-alpha (human)") +AnnotationAssertion(Annotation( "UniProtKB:P10147") "PAT 464.1 (human)") +AnnotationAssertion(Annotation( "UniProtKB:P10147") "SIS-beta (human)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hCCL3") +AnnotationAssertion(Annotation( "UniProtKB:P10147") "macrophage inflammatory protein 1-alpha (human)") +AnnotationAssertion(Annotation( "UniProtKB:P10147") "small-inducible cytokine A3 (human)") +AnnotationAssertion(Annotation( "UniProtKB:P10147") "tonsillar lymphocyte LD78 alpha protein (human)") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:P10147") Annotation( ) "CCL3") +AnnotationAssertion(Annotation( "UniProtKB:P10147") Annotation( ) "G0S19-1") +AnnotationAssertion(Annotation( "UniProtKB:P10147") Annotation( ) "MIP1A") +AnnotationAssertion(Annotation( "UniProtKB:P10147") Annotation( ) "SCYA3") +AnnotationAssertion( "PR:P10147") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "C-C motif chemokine 3 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (non-secretory ribonuclease (human)) AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:P10153") "A non-secretory ribonuclease that is encoded in the genome of human.") @@ -123078,6 +123182,30 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (C-C motif chemokine 3 (mouse)) + +AnnotationAssertion(Annotation( "PRO:WCB") "A C-C motif chemokine 3 that is encoded in the genome of mouse.") +AnnotationAssertion( "UniProtKB:P10855") +AnnotationAssertion(Annotation( "UniProtKB:P10855") "L2G25B (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:P10855") "MIP-1-alpha (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:P10855") "SIS-alpha (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:P10855") "TY-5 (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:P10855") "heparin-binding chemotaxis protein (mouse)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mCCL3") +AnnotationAssertion(Annotation( "UniProtKB:P10855") "macrophage inflammatory protein 1-alpha (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:P10855") "small-inducible cytokine A3 (mouse)") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:P10855") Annotation( ) "Ccl3") +AnnotationAssertion(Annotation( "UniProtKB:P10855") Annotation( ) "Mip1a") +AnnotationAssertion(Annotation( "UniProtKB:P10855") Annotation( ) "Scya3") +AnnotationAssertion( "PR:P10855") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "C-C motif chemokine 3 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (T-cell surface glycoprotein CD8 beta chain (human)) AnnotationAssertion(Annotation( "PRO:CNA") Annotation( "UniProtKB:P10966") "A T-cell surface glycoprotein CD8 beta chain that is encoded in the genome of human.") @@ -123250,10 +123378,10 @@ SubClassOf( ObjectSomeValuesFrom( "PRO:DNx") Annotation( "UniProtKB:P11684") "A uteroglobin that is encoded in the genome of human.") AnnotationAssertion( "UniProtKB:P11684") AnnotationAssertion(Annotation( "UniProtKB:P11684") "CCPBP (human)") +AnnotationAssertion(Annotation( "UniProtKB:P11684") "Club cell phospholipid-binding protein (human)") +AnnotationAssertion(Annotation( "UniProtKB:P11684") "Club cells 10 kDa secretory protein (human)") AnnotationAssertion(Annotation( "UniProtKB:P11684") "UP-1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P11684") "UP1 (human)") -AnnotationAssertion(Annotation( "UniProtKB:P11684") "clara cell phospholipid-binding protein (human)") -AnnotationAssertion(Annotation( "UniProtKB:P11684") "clara cells 10 kDa secretory protein (human)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hSCGB1A1") AnnotationAssertion(Annotation( "UniProtKB:P11684") "secretoglobin family 1A member 1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P11684") "urinary protein 1 (human)") @@ -127232,10 +127360,10 @@ AnnotationAssertion(Annotation( "UniProtKB:Q06318") AnnotationAssertion(Annotation( "UniProtKB:Q06318") "CC10 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:Q06318") "CCPBP (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q06318") "Club cell 17 kDa protein (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q06318") "Club cell phospholipid-binding protein (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q06318") "Club cells 10 kDa secretory protein (mouse)") AnnotationAssertion(Annotation( "UniProtKB:Q06318") "PCB-binding protein (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:Q06318") "clara cell 17 kDa protein (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:Q06318") "clara cell phospholipid-binding protein (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:Q06318") "clara cells 10 kDa secretory protein (mouse)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mSCGB1A1") AnnotationAssertion(Annotation( "UniProtKB:Q06318") "secretoglobin family 1A member 1 (mouse)") AnnotationAssertion( "protein") diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 5fc4d25fa..56a448b76 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-06-16") + +Annotation(owl:versionInfo "2023-06-20")