From a3f3f034fef1b2f5d80e5ff3cc1930f4107ea212 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Wed, 11 Dec 2024 16:09:52 +0200 Subject: [PATCH 1/3] Remove BFO from imports --- src/ontology/Makefile | 4 ++-- src/ontology/hp-odk.yaml | 11 +++++++++++ 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 48b70659a..b48d3eda5 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 96cc08421fe1323e389345fd556c8f1d18ca491947a1f2b227f9c10a39cb0740 +CONFIG_HASH= 0fcd636feea85fce01a9e5009487aad06aedf4ba32833cb10c92bcf68fbc2cc2 # ---------------------------------------- @@ -384,7 +384,7 @@ $(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED) $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \ - remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" \ + remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" \ extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \ remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select annotation-properties \ query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ diff --git a/src/ontology/hp-odk.yaml b/src/ontology/hp-odk.yaml index 692c4d4d1..bc633100c 100644 --- a/src/ontology/hp-odk.yaml +++ b/src/ontology/hp-odk.yaml @@ -34,6 +34,17 @@ import_group: - - - + - + - + - + - + - + - + - + - + - + - + - - - - From 88fd57f9643d7ebf3e26a2d51d303b55644ba79c Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Wed, 11 Dec 2024 16:10:09 +0200 Subject: [PATCH 2/3] Refresh imports --- src/ontology/imports/merged_import.owl | 3788 +++++++++--------------- 1 file changed, 1420 insertions(+), 2368 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 66409cee3..c41b799c3 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,20 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-08-12") - -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) + +Annotation(owl:versionInfo "2024-12-11") + Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -403,7 +392,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1467,8 +1455,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2003,7 +1989,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2012,6 +1997,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2083,7 +2069,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2402,6 +2387,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2432,6 +2418,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2546,7 +2533,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2650,6 +2636,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2688,7 +2675,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2951,6 +2937,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2998,7 +2985,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3021,6 +3007,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3035,6 +3023,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3055,6 +3044,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3311,9 +3301,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3338,7 +3325,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3373,26 +3359,24 @@ 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()) -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()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3420,7 +3404,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3457,6 +3440,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3573,30 +3557,11 @@ 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()) -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()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3777,8 +3742,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3790,22 +3753,18 @@ 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()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3815,10 +3774,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3838,11 +3795,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3852,7 +3805,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3863,6 +3815,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3874,6 +3827,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3949,9 +3904,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3977,15 +3929,8 @@ 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()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4034,6 +3979,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4104,9 +4051,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4118,15 +4065,9 @@ 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()) Declaration(Class()) Declaration(Class()) @@ -4136,8 +4077,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4152,15 +4091,13 @@ 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()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4193,6 +4130,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4238,9 +4176,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4322,6 +4257,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4343,16 +4282,16 @@ 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()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4364,11 +4303,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4382,6 +4317,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4399,8 +4335,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4483,8 +4417,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4502,6 +4434,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4525,8 +4459,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4534,9 +4468,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4546,8 +4477,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4581,8 +4510,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4857,7 +4786,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4881,6 +4809,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4982,6 +4912,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4992,10 +4923,15 @@ 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()) Declaration(Class()) Declaration(Class()) @@ -5024,8 +4960,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5083,6 +5017,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5097,10 +5032,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5145,6 +5076,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5152,12 +5084,14 @@ 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()) Declaration(Class()) @@ -5172,10 +5106,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5243,6 +5175,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5253,6 +5186,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5282,14 +5216,12 @@ 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()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5302,9 +5234,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5338,7 +5267,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5397,9 +5325,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5492,7 +5417,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5582,6 +5506,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5925,7 +5852,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6182,7 +6108,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6233,6 +6158,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6302,6 +6228,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6500,6 +6427,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -7605,7 +7533,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9228,7 +9155,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9270,7 +9196,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12043,6 +11968,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12366,6 +12292,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12454,20 +12381,11 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) -Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty(owl:deprecated)) ############################ # Annotation Properties ############################ -# Annotation Property: (definition) - -AnnotationAssertion(rdfs:label "definition") - -# Annotation Property: (term replaced by) - -AnnotationAssertion(rdfs:label "term replaced by") - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -12561,6 +12479,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -12793,58 +12715,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (subset_property) - -AnnotationAssertion(rdfs:label "subset_property") - -# Annotation Property: (consider) - -AnnotationAssertion(rdfs:label "consider") - -# Annotation Property: (creation date) - -AnnotationAssertion(rdfs:label "creation date") - -# Annotation Property: (has_alternative_id) - -AnnotationAssertion(rdfs:label "has_alternative_id") - -# Annotation Property: (has_broad_synonym) - -AnnotationAssertion(rdfs:label "has_broad_synonym") - -# Annotation Property: (database_cross_reference) - -AnnotationAssertion(rdfs:label "database_cross_reference") - -# Annotation Property: (has_exact_synonym) - -AnnotationAssertion(rdfs:label "has_exact_synonym") - -# Annotation Property: (has_narrow_synonym) - -AnnotationAssertion(rdfs:label "has_narrow_synonym") - -# Annotation Property: (has_obo_format_version) - -AnnotationAssertion(rdfs:label "has_obo_format_version") - -# Annotation Property: (has_related_synonym) - -AnnotationAssertion(rdfs:label "has_related_synonym") - -# Annotation Property: (id) - -AnnotationAssertion(rdfs:label "id") - -# Annotation Property: (in_subset) - -AnnotationAssertion(rdfs:label "in_subset") - -# Annotation Property: (shorthand) - -AnnotationAssertion(rdfs:label "shorthand") - ############################ # Object Properties @@ -12853,30 +12723,22 @@ AnnotationAssertion(rdfs:label (part of) AnnotationAssertion( "a core relation that holds between a part and its whole"@en) -AnnotationAssertion( "BFO:0000050") -AnnotationAssertion( "part_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "part_of") AnnotationAssertion(rdfs:label "part of"@en) -AnnotationAssertion(rdfs:label "part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() -# Object Property: (has_part) +# Object Property: (has part) AnnotationAssertion( "a core relation that holds between a whole and its part"@en) -AnnotationAssertion( "BFO:0000051") -AnnotationAssertion( "has_part") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "has_part") AnnotationAssertion(rdfs:label "has part"@en) -AnnotationAssertion(rdfs:label "has_part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -12888,8 +12750,6 @@ AnnotationAssertion(rdfs:label "pre SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (precedes) @@ -12898,8 +12758,6 @@ AnnotationAssertion( "precedes"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (occurs in) @@ -12910,8 +12768,6 @@ AnnotationAssertion( "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:label "occurs in"@en) InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (contains process) @@ -12945,22 +12801,17 @@ FunctionalObjectProperty() AnnotationAssertion( "Inverse of characteristic_of"@en) AnnotationAssertion(rdfs:label "has characteristic"@en) InverseFunctionalObjectProperty() -ObjectPropertyRange( ) # Object Property: (participates in) AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) AnnotationAssertion(rdfs:label "participates in"@en) InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (has participant) AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion(rdfs:label "has participant"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (quality of) @@ -12983,15 +12834,12 @@ InverseObjectProperties( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) AnnotationAssertion(rdfs:label "has quality"@en) SubObjectPropertyOf( ) -ObjectPropertyRange( ) # Object Property: (has role) AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) AnnotationAssertion(rdfs:label "has role"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (location of) @@ -13006,8 +12854,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "located in"@en) TransitiveObjectProperty() -ObjectPropertyDomain( ObjectIntersectionOf( ObjectComplementOf())) -ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) # Object Property: (2D boundary of) @@ -13021,8 +12867,6 @@ InverseObjectProperties( "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity"@en) AnnotationAssertion(rdfs:label "has 2D boundary"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (innervated_by) @@ -13046,8 +12890,6 @@ AnnotationAssertion( "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.") AnnotationAssertion(rdfs:label "bounding layer of"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -ObjectPropertyRange( ) # Object Property: (before or simultaneous with) @@ -13151,8 +12993,6 @@ AnnotationAssertion( "continuous with"@en) SubObjectPropertyOf( ) SymmetricObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (derived by descent from) @@ -13206,7 +13046,6 @@ ObjectPropertyRange( ObjectSomeValues AnnotationAssertion( "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.") AnnotationAssertion(rdfs:label "connects"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ObjectSomeValuesFrom( )) # Object Property: (attached to part of) @@ -13246,8 +13085,6 @@ SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (develops into) @@ -13265,8 +13102,6 @@ AnnotationAssertion( "expressed in"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyDomain( ObjectUnionOf( )) ObjectPropertyRange( ) # Object Property: (directly develops from) @@ -13297,8 +13132,6 @@ AnnotationAssertion(rdfs:label "regu SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (negatively regulates) @@ -13329,8 +13162,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capable of"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (capable of part of) @@ -13354,8 +13185,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "adjacent to"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (surrounds) @@ -13369,8 +13198,6 @@ SubObjectPropertyOf( ) AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") AnnotationAssertion(rdfs:label "temporally related to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (starts) @@ -13427,8 +13254,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has start location"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (has end location) @@ -13436,8 +13261,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has end location"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (has output) @@ -13505,8 +13328,6 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "developmentally preceded by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (acts upstream of) @@ -13603,8 +13424,6 @@ SubObjectPropertyOf( "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.") AnnotationAssertion(rdfs:label "genomically related to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (regulated by) @@ -13613,8 +13432,6 @@ AnnotationAssertion( "regulated by"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (negatively regulated by) @@ -13634,8 +13451,6 @@ SubObjectPropertyOf( "A relationship that holds via some process of localization") AnnotationAssertion(rdfs:label "related via localization to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (has target end location) @@ -13710,8 +13525,6 @@ SubObjectPropertyOf( "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.") AnnotationAssertion(rdfs:label "in branching relationship with"@en) SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (tributary of) @@ -13836,16 +13649,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "composed primarily of") SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (has part that occurs in) AnnotationAssertion( "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part that occurs in") -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (receives input from) @@ -13861,8 +13670,6 @@ SubObjectPropertyOf( (relation between physical entity and a process or stage) AnnotationAssertion(rdfs:label "relation between physical entity and a process or stage") -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (existence starts during) @@ -13948,8 +13755,6 @@ InverseObjectProperties( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") AnnotationAssertion(rdfs:label "causal relation between processes") SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (depends on) @@ -14000,8 +13805,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "conduit for") SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (lumen of) @@ -14009,7 +13812,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lumen of") SubObjectPropertyOf( ) -ObjectPropertyRange( ) # Object Property: (luminal space of) @@ -14017,15 +13819,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "luminal space of") SubObjectPropertyOf( ) -ObjectPropertyDomain( ) # Object Property: (has modifier) AnnotationAssertion( "A relation that holds between an attribute or a qualifier and another attribute.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has modifier") -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (skeleton of) @@ -14048,8 +13847,6 @@ SubObjectPropertyOf( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") AnnotationAssertion(rdfs:label "causal relation between material entity and a process") SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (capable of regulating) @@ -14082,16 +13879,12 @@ AnnotationAssertion( "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") AnnotationAssertion(rdfs:label "produces"@en) InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (produced by) AnnotationAssertion( "a produced_by b iff some process that occurs_in b has_output a.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "produced by"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) # Object Property: (causally upstream of or within, negative effect) @@ -14326,22 +14119,6 @@ SubObjectPropertyOf( < # Classes ############################ -# Class: () - -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: () - -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: () - -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: () - -DisjointClasses( ObjectSomeValuesFrom( )) - # Class: (electron) AnnotationAssertion( "Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.") @@ -15027,7 +14804,7 @@ SubClassOf( ObjectSomeValuesFrom( (alpha-hydroxy ketone) -AnnotationAssertion( "An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety.") +AnnotationAssertion( "A ketone containing a hydroxy group on the alpha-carbon relative to the C=O group.") AnnotationAssertion(Annotation( "ChEBI") "alpha-hydroxy ketones") AnnotationAssertion(Annotation( "ChEBI") "alpha-hydroxy-ketone") AnnotationAssertion(Annotation( "ChEBI") "alpha-hydroxy-ketones") @@ -15036,8 +14813,8 @@ AnnotationAssertion(Annotation( "CHEBI:139588") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "alpha-hydroxy ketone") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (retinoid anion) @@ -20959,7 +20736,6 @@ AnnotationAssertion( "KEGG:C02465") AnnotationAssertion( "KEGG:D08128") AnnotationAssertion( "LINCS:LSM-3991") -AnnotationAssertion( "MetaCyc:CPD-10813") AnnotationAssertion( "PDBeChem:T3") AnnotationAssertion( "Wikipedia:Triiodothyronine") AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "3,3',5-triiodo-L-thyronine") @@ -20967,8 +20743,10 @@ AnnotationAssertion(Annotation( "KEGG_COMPOUND") "3,5,3'-Triiodothyronine") AnnotationAssertion(Annotation( "PDBeChem") "3,5,3'TRIIODOTHYRONINE") AnnotationAssertion(Annotation( "IUPAC") "4-(4-hydroxy-3-iodophenoxy)-3,5-diiodo-L-phenylalanine") +AnnotationAssertion(Annotation( "HMDB") "L-3,3',5-triiodothyronine") AnnotationAssertion(Annotation( "KEGG_COMPOUND") "L-3,5,3'-Triiodothyronine") AnnotationAssertion(Annotation( "ChemIDplus") "L-T3") +AnnotationAssertion(Annotation( "HMDB") "L-triiodothyronine") AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Liothyronine") AnnotationAssertion(Annotation( "IUPAC") "O-(4-hydroxy-3-iodophenyl)-3,5-diiodo-L-tyrosine") AnnotationAssertion(Annotation( "ChEBI") "T3") @@ -22214,7 +21992,7 @@ SubClassOf( ObjectSomeValuesFrom( (NMR chemical shift reference compound) -AnnotationAssertion( "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing.") +AnnotationAssertion( "Any compound that produces a peak used as reference frequency in the delta chemical shift scale.") AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift reference compounds") AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift standard") AnnotationAssertion(Annotation( "ChEBI") "NMR chemical shift standards") @@ -22412,18 +22190,6 @@ AnnotationAssertion(rdfs:label "chl SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (sialylglycoconjugate anion) - -AnnotationAssertion( "A sialylglycoconjugate where the composition of the glycoconjugate represented with an R is not defined, can be an oligosaccharide, a glycoprotein or a glycolipid.") -AnnotationAssertion(Annotation( "SUBMITTER") "Neu5Ac-glycoconjugate anion") -AnnotationAssertion(Annotation( "UniProt") "a sialoglycoconjugate") -AnnotationAssertion(Annotation( "SUBMITTER") "a sialoglycoconjugate anion") -AnnotationAssertion( "CHEBI:231691") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "sialylglycoconjugate anion") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (chromanol) AnnotationAssertion( "Any member of the class of chromanes that is chromane substituted by one or more hydroxy groups.") @@ -24717,15 +24483,14 @@ SubClassOf( ObjectSomeValuesFrom( (serine family amino acid) -AnnotationAssertion( "An L-alpha-amino acid which is biosynthesised from 3-phosphoglycerate (i.e. serine, glycine, cysteine and homocysteine). A closed class.") +AnnotationAssertion( "An alpha-amino acid which is biosynthesised from 3-phosphoglycerate (i.e. serine, glycine, cysteine and homocysteine). A closed class.") AnnotationAssertion(Annotation( "ChEBI") "3-phosphoglycerate family amino acid") AnnotationAssertion(Annotation( "ChEBI") "3-phosphoglycerate family amino acids") AnnotationAssertion(Annotation( "ChEBI") "serine family amino acids") AnnotationAssertion( "CHEBI:26650") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "serine family amino acid") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (sesquiterpenoid) @@ -26450,18 +26215,18 @@ AnnotationAssertion( "CHEBI:26669") AnnotationAssertion( "CHEBI:36525") AnnotationAssertion( "CHEBI:5274") -AnnotationAssertion( "KEGG:C01808") +AnnotationAssertion( "MetaCyc:Gangliosides") AnnotationAssertion( "Wikipedia:Ganglioside") -AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Ganglioside") +AnnotationAssertion(Annotation( "ChEBI") "ganglioside") AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "sialoglycosphingolipids") AnnotationAssertion(Annotation( "ChEBI") "gangliosides") -AnnotationAssertion(Annotation( "LIPID_MAPS") "gangliosides") +AnnotationAssertion(Annotation( "ChEBI") "sialoglycosphingolipid") AnnotationAssertion( "CHEBI:28892") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ganglioside") SubClassOf( ) -SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: ((R)-adrenaline) @@ -29860,7 +29625,7 @@ SubClassOf( ObjectSomeValuesFrom( (alpha-amino-acid anion) AnnotationAssertion( "An amino-acid anion obtained by deprotonation of any alpha-amino acid.") -AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid anion") +AnnotationAssertion(Annotation( "ChEBI") "alpha-amino acid anion") AnnotationAssertion(Annotation( "ChEBI") "alpha-amino acid anions") AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid anions") AnnotationAssertion( "CHEBI:33558") @@ -30325,8 +30090,8 @@ SubClassOf( (amino-acid cation) -AnnotationAssertion(Annotation( "ChEBI") "amino-acid cation") AnnotationAssertion(Annotation( "ChEBI") "amino acid cation") +AnnotationAssertion(Annotation( "ChEBI") "amino acid cations") AnnotationAssertion(Annotation( "ChEBI") "amino-acid cations") AnnotationAssertion( "CHEBI:33703") AnnotationAssertion( ) @@ -30384,6 +30149,7 @@ SubClassOf( ObjectSomeValuesFrom( "When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.") AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "amino-acid residue") AnnotationAssertion(Annotation( "ChEBI") "amino acid residue") +AnnotationAssertion(Annotation( "ChEBI") "amino acid residues") AnnotationAssertion(Annotation( "JCBN") "amino-acid residues") AnnotationAssertion( "CHEBI:33708") AnnotationAssertion( ) @@ -30424,7 +30190,7 @@ SubClassOf( ObjectSomeValuesFrom( (alpha-amino-acid cation) -AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid cation") +AnnotationAssertion(Annotation( "ChEBI") "alpha-amino acid cation") AnnotationAssertion(Annotation( "ChEBI") "alpha-amino acid cations") AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid cations") AnnotationAssertion( "CHEBI:33719") @@ -31138,13 +30904,15 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (amino acid zwitterion) +# Class: (amino-acid zwitterion) AnnotationAssertion( "The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group.") -AnnotationAssertion(Annotation( "ChEBI") "amino acid zwitterion") +AnnotationAssertion(Annotation( "ChEBI") "amino acid zwitterion") +AnnotationAssertion(Annotation( "ChEBI") "amino acid zwitterions") +AnnotationAssertion(Annotation( "ChEBI") "amino-acid zwitterions") AnnotationAssertion( "CHEBI:35238") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "amino acid zwitterion") +AnnotationAssertion(rdfs:label "amino-acid zwitterion") SubClassOf( ) # Class: (serine zwitterion) @@ -33208,7 +32976,7 @@ SubClassOf( (amino-acid anion) -AnnotationAssertion(Annotation( "ChEBI") "amino-acid anion") +AnnotationAssertion(Annotation( "ChEBI") "amino acid anion") AnnotationAssertion(Annotation( "ChEBI") "amino acid anions") AnnotationAssertion(Annotation( "ChEBI") "amino-acid anions") AnnotationAssertion( "CHEBI:37022") @@ -36694,24 +36462,6 @@ AnnotationAssertion( "sterol methyltransferase inhibitor") SubClassOf( ) -# Class: (oxyketone) - -AnnotationAssertion( "A compound with the general formula R2C=O (R=/=H) where one or more of the R groups contains an oxy (-O-) group.") -AnnotationAssertion(Annotation( "ChEBI") "oxyketones") -AnnotationAssertion( "CHEBI:52395") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "oxyketone") -SubClassOf( ) - -# Class: (alpha-oxyketone) - -AnnotationAssertion( "An oxyketone with the general formula R2C(=O) (R=/=H) where one or more of the R groups contains an oxy (-O-) group and the oxy and carbonyl groups are bonded to the same carbon atom.") -AnnotationAssertion(Annotation( "ChEBI") "alpha-oxyketones") -AnnotationAssertion( "CHEBI:52396") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "alpha-oxyketone") -SubClassOf( ) - # Class: (EC 3.2.1.* (glycosidase) inhibitor) AnnotationAssertion( "An EC 3.2.* (glycosylase) inhibitor that interferes with the action of any glycosidase (i.e. enzymes hydrolysing O- and S-glycosyl compounds, EC 3.2.1.*).") @@ -36799,7 +36549,7 @@ SubClassOf( (3,3',5-triiodo-L-thyronine zwitterion) AnnotationAssertion( "The amino acid zwitterion formed from 3,3',5-triiodo-L-thyronine by tranfer of a proton from the carboxy group to the amino group. It is the major species at pH 7.3.") -AnnotationAssertion( "MetaCyc:CPD-10813") +AnnotationAssertion( "MetaCyc:LIOTHYRONINE") AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "(2S)-2-azaniumyl-3-[4-(4-hydroxy-3-iodophenoxy)-3,5-diiodophenyl]propanoate") AnnotationAssertion(Annotation( "ChEMBL") "(S)-2-Amino-3-[4-(4-hydroxy-3-iodo-phenoxy)-3,5-diiodo-phenyl]-propionic acid") AnnotationAssertion(Annotation( "UniProt") "3,3',5-triiodo-L-thyronine") @@ -36836,7 +36586,7 @@ SubClassOf( "The all-cis-isomer of a C22 polyunsaturated fatty acid having four double bonds in the 7-, 10-, 13- and 16-positions. One of the most abundant fatty acids in the early human brain.") AnnotationAssertion( "HMDB:HMDB0002226") AnnotationAssertion( "KEGG:C16527") -AnnotationAssertion( "Wikipedia:Adrenic_acid") +AnnotationAssertion( "Wikipedia:Docosatetraenoic_acid") AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "(7Z,10Z,13Z,16Z)-docosa-7,10,13,16-tetraenoic acid") AnnotationAssertion(Annotation( "KEGG_COMPOUND") "(7Z,10Z,13Z,16Z)-Docosa-7,10,13,16-tetraenoic acid") AnnotationAssertion(Annotation( "KEGG_COMPOUND") "7,10,13,16-Docosatetraenoic acid") @@ -37192,6 +36942,7 @@ AnnotationAssertion(Annotation( "CHEBI:57932") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "D-methionine zwitterion") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -37475,7 +37226,7 @@ SubClassOf( ObjectSomeValuesFrom( (N-acyl-L-aspartate(2-)) AnnotationAssertion( "Conjugate base of an N-acyl-L-aspartic acid.") -AnnotationAssertion(Annotation( "UniProt") "N-acyl-L-aspartate") +AnnotationAssertion(Annotation( "UniProt") "an N-acyl-L-aspartate") AnnotationAssertion( "CHEBI:58497") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "N-acyl-L-aspartate(2-)") @@ -39224,7 +38975,6 @@ AnnotationAssertion(Annotation( "ChEBI") "amino-acid anion residues") AnnotationAssertion(Annotation( "ChEBI") "anionic amino acid residue") AnnotationAssertion(Annotation( "ChEBI") "anionic amino acid residues") -AnnotationAssertion(Annotation( "ChEBI") "anionic amino-acid residues") AnnotationAssertion( "CHEBI:64898") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anionic amino-acid residue") @@ -41085,14 +40835,17 @@ AnnotationAssertion(rdfs:label "pyr SubClassOf( ) SubClassOf( ) -# Class: (alpha-amino acid zwitterion) +# Class: (alpha-amino-acid zwitterion) -AnnotationAssertion( "An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3.") +AnnotationAssertion( "An amino acid-zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3.") AnnotationAssertion( "CHEBI:83409") +AnnotationAssertion(Annotation( "ChEBI") "alpha-amino acid zwitterion") +AnnotationAssertion(Annotation( "ChEBI") "alpha-amino acid zwitterions") +AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid zwitterions") AnnotationAssertion(Annotation( "UniProt") "an alpha-amino acid") AnnotationAssertion( "CHEBI:78608") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "alpha-amino acid zwitterion") +AnnotationAssertion(rdfs:label "alpha-amino-acid zwitterion") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -41247,6 +41000,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anionic ganglioside") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trivalent inorganic anion) @@ -41422,15 +41176,17 @@ AnnotationAssertion( "non-proteinogenic amino acid") SubClassOf( ) -# Class: (amino acid derivative) +# Class: (amino-acid derivative) AnnotationAssertion( "Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues.") AnnotationAssertion( "CHEBI:25359") +AnnotationAssertion(Annotation( "ChEBI") "amino acid derivative") AnnotationAssertion(Annotation( "ChEBI") "amino acid derivatives") +AnnotationAssertion(Annotation( "ChEBI") "amino-acid derivatives") AnnotationAssertion(Annotation( "ChEBI") "modified amino acids") AnnotationAssertion( "CHEBI:83821") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "amino acid derivative") +AnnotationAssertion(rdfs:label "amino-acid derivative") SubClassOf( ) # Class: (non-proteinogenic L-alpha-amino acid) @@ -42074,7 +41830,6 @@ AnnotationAssertion( "WBbt:0006799") AnnotationAssertion(rdfs:label "spermatocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -42090,8 +41845,8 @@ AnnotationAssertion( "nematoblast") AnnotationAssertion(rdfs:label "spermatid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -42111,7 +41866,7 @@ AnnotationAssertion( "spermatozoon") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sperm") -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42138,6 +41893,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "female germ cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42160,9 +41916,7 @@ AnnotationAssertion( "oogonium") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "oocyte") -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (oogonial cell) @@ -42172,7 +41926,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "oogonial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -42191,7 +41944,6 @@ AnnotationAssertion(Annotation( "neuron neural crest derived") AnnotationAssertion(rdfs:label "neural crest derived neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42199,8 +41951,8 @@ SubClassOf( ObjectSomeValuesFrom( ) AnnotationAssertion(rdfs:label "glioblast") -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuroblast (sensu Vertebrata)) @@ -42226,6 +41978,7 @@ AnnotationAssertion( "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’.") AnnotationAssertion(rdfs:label "stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42325,6 +42078,7 @@ AnnotationAssertion(rdfs:label "mono EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -42452,7 +42206,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "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 "fibroblast") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42463,7 +42216,6 @@ AnnotationAssertion( "FMA:66783") AnnotationAssertion( "chrondoplast") AnnotationAssertion(rdfs:label "chondroblast") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42512,7 +42264,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ciliated cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell) @@ -42528,7 +42281,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -42565,7 +42318,6 @@ AnnotationAssertion(rdfs:label "bloo EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (non-branched duct epithelial cell) @@ -42583,28 +42335,33 @@ SubClassOf( (squamous epithelial cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any epithelial cell that is part of some squamous epithelium.") AnnotationAssertion( "CALOHA:TS-1249") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "squamous epithelial cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell) -AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") "A flattened epithelial cell of mesenchymal origin that lines the serous cavity.") +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") Annotation( "PMID:26106328") "A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement.") AnnotationAssertion( "FMA:66773") AnnotationAssertion( "mesotheliocyte") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(Annotation( "PMID:26106328") rdfs:comment "Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport.") AnnotationAssertion(rdfs:label "mesothelial cell") SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stratified epithelial cell) +AnnotationAssertion(Annotation( "Wikipedia:Epithelium") Annotation( "doi:/10.1016/B978-0-12-410424-2.00003-2") Annotation( "https://www.biologyonline.com/dictionary/stratified-epithelium") "An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stratified epithelial cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42613,7 +42370,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:add") "A cell which moves among different tissues of the body, via blood, lymph, or other medium.") AnnotationAssertion(rdfs:label "circulating cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood cell) @@ -42689,6 +42446,7 @@ AnnotationAssertion(rdfs:label "gran EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -42702,7 +42460,6 @@ SubClassOf( ObjectSomeValuesFrom( ) AnnotationAssertion(rdfs:label "neuron associated cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42724,6 +42481,7 @@ AnnotationAssertion(rdfs:label "mast EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -42832,6 +42590,7 @@ AnnotationAssertion(owl:deprecated " AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:tfm") Annotation( "ISBN:0781735149") "A vertebrate phagocyte with a single nucleus.") AnnotationAssertion( "BTO:0001433") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000113") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mononuclear phagocyte") @@ -42859,14 +42618,13 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].") AnnotationAssertion(rdfs:label "endothelial cell") -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (CNS neuron (sensu Vertebrata)) AnnotationAssertion(rdfs:label "CNS neuron (sensu Vertebrata)") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -42893,15 +42651,17 @@ SubClassOf( (Purkinje cell) -AnnotationAssertion(Annotation( "MESH:D011689") "The output neuron of the cerebellar cortex.") +AnnotationAssertion(Annotation( "MESH:D011689") Annotation( "PMID:12907269") Annotation( "PMID:14568361") Annotation( "PMID:31424738") Annotation( "PMID:33288911") Annotation( "PMID:38168772") "An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as \"simple spikes,\" and climbing fibres, which modulate infrequent calcium spike activity known as \"complex spikes\". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress.") AnnotationAssertion( "BTO:0001011") AnnotationAssertion( "CALOHA:TS-0845") AnnotationAssertion( "FMA:67969") -AnnotationAssertion( "Purkinje neuron") -AnnotationAssertion( "Purkinje's cell") -AnnotationAssertion( "cerebellar Purkinje cell") -AnnotationAssertion( "cerebellum Purkinje cell") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000121") +AnnotationAssertion(Annotation( "PMID:28821816") "Purkinje neuron") +AnnotationAssertion(Annotation( "https://doi.org/10.1016/j.proghi.2004.07.002") "cerebellar Purkinje cell") +AnnotationAssertion(Annotation( "PMID:38168772") Annotation( ) "PC") +AnnotationAssertion(Annotation( "PMID:28821816") Annotation( ) "PN") AnnotationAssertion( ) +AnnotationAssertion(Annotation( "PMID:17535929") Annotation( "PMID:27215193") Annotation( "PMID:37426070") Annotation( "https://doi.org/10.1016/j.stem.2023.11.013") rdfs:comment "Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024).") AnnotationAssertion(rdfs:label "Purkinje cell") SubClassOf( ) SubClassOf( ) @@ -42913,7 +42673,6 @@ SubClassOf( ObjectSomeValuesFrom( ) AnnotationAssertion(rdfs:label "neuron associated cell (sensu Vertebrata)") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (glial cell) @@ -42922,6 +42681,7 @@ AnnotationAssertion(Annotation( "BTO:0002606") AnnotationAssertion( "CALOHA:TS-0415") AnnotationAssertion( "FMA:54536") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000125") AnnotationAssertion( "neuroglial cell") AnnotationAssertion( "neuroglia") AnnotationAssertion( ) @@ -42976,7 +42736,7 @@ SubClassOf( ObjectSomeValuesFrom( (microglial cell) -AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "ISBN:0721601464") Annotation( "MESH:D017628") Annotation( "PMID:11517395") Annotation( "PMID:12430718") Annotation( "PMID:14561199") Annotation( "PMID:14612429") Annotation( "PMID:16177057") Annotation( "PMID:19461673") Annotation( "PMID:2089275") Annotation( "http://en.wikipedia.org/wiki/Microglia") "A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive.") +AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "ISBN:0721601464") Annotation( "MESH:D017628") Annotation( "PMID:11517395") Annotation( "PMID:12430718") Annotation( "PMID:14561199") Annotation( "PMID:14612429") Annotation( "PMID:16177057") Annotation( "PMID:19461673") Annotation( "PMID:2089275") Annotation( "http://en.wikipedia.org/wiki/Microglia") "A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive.") AnnotationAssertion( "brain macrophage") AnnotationAssertion( "BTO:0000078") AnnotationAssertion( "BTO:0000962") @@ -42993,6 +42753,7 @@ AnnotationAssertion(rdfs:label "micr EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -43043,7 +42804,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "adipocyte") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43103,8 +42863,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -43144,6 +42904,7 @@ AnnotationAssertion( "exocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (glycosaminoglycan secreting cell) @@ -43192,15 +42953,18 @@ SubClassOf( (goblet cell) -AnnotationAssertion(Annotation( "MESH:D020397") "A cell of the epithelial lining that produce and secrete mucins.") +AnnotationAssertion(Annotation( "MESH:D020397") Annotation( "http://en.wikipedia.org/wiki/Goblet_cell") "A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane.") AnnotationAssertion( "BTO:0001540") AnnotationAssertion( "FMA:13148") AnnotationAssertion( "http://en.wikipedia.org/wiki/Goblet_cell") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000160") AnnotationAssertion( "chalice cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "goblet cell") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endocrine cell) @@ -43213,6 +42977,7 @@ AnnotationAssertion( "endocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) @@ -43222,6 +42987,7 @@ AnnotationAssertion(Annotation( "BTO:0003865") AnnotationAssertion( "FMA:62930") AnnotationAssertion( "MESH:D019858") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000164") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enteroendocrine cell") SubClassOf( ) @@ -43250,6 +43016,7 @@ SubClassOf( "MESH:D019439") "A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system.") AnnotationAssertion( "BTO:0000259") AnnotationAssertion( "FMA:69263") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000166") AnnotationAssertion( "phaeochromocyte") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chromaffin cell") @@ -43272,6 +43039,7 @@ AnnotationAssertion(rdfs:label "insu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (type B pancreatic cell) @@ -43382,11 +43150,11 @@ AnnotationAssertion( "EMAPA:29655") AnnotationAssertion( "FMA:72297") AnnotationAssertion( "MESH:D007985") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000178") AnnotationAssertion( "interstitial cell of Leydig") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that the Amphibian Anatomy Ontology (AA) has a class 'leydig cells' but this is unrelated") AnnotationAssertion(rdfs:label "Leydig cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43398,11 +43166,11 @@ AnnotationAssertion(Annotation( "BTO:0000575") AnnotationAssertion( "CALOHA:TS-0454") AnnotationAssertion( "FMA:14515") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000182") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive.") AnnotationAssertion(rdfs:label "hepatocyte") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43429,8 +43197,8 @@ AnnotationAssertion( "myocyte") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle cell") -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43446,7 +43214,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell of skeletal muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell) @@ -43474,7 +43242,7 @@ AnnotationAssertion( "receptor cell") AnnotationAssertion(rdfs:label "sensory receptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -43536,15 +43304,16 @@ SubClassOf( ObjectSomeValuesFrom( (photoreceptor cell) -AnnotationAssertion(Annotation( "MESH:D010786") "A cell specialized to detect and transduce light.") +AnnotationAssertion(Annotation( "MESH:D010786") "A cell specialized in detecting light stimuli that are involved in visual perception.") AnnotationAssertion( "BTO:0001060") AnnotationAssertion( "CALOHA:TS-0868") AnnotationAssertion( "FMA:86740") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "photoreceptor cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (electrically active cell) @@ -43603,6 +43372,7 @@ AnnotationAssertion(Annotation( "FMA:72549") AnnotationAssertion( "ectoderm cell") AnnotationAssertion(rdfs:label "ectodermal cell") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43614,6 +43384,7 @@ AnnotationAssertion( "mesoderm cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesodermal cell") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43623,6 +43394,7 @@ AnnotationAssertion(Annotation( "FMA:72555") AnnotationAssertion( "endoderm cell") AnnotationAssertion(rdfs:label "endodermal cell") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43642,27 +43414,18 @@ DisjointClasses( "FB:ma") Annotation( "GOC:tfm") "A cell with a single nucleus.") AnnotationAssertion(rdfs:label "single nucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (binucleate cell) - -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that has characteristic some binucleate.") -AnnotationAssertion(rdfs:label "binucleate cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (multinucleate cell) -AnnotationAssertion(Annotation( "FB:ma") "A cell with more than one nucleus.") -AnnotationAssertion( "AEO:0000203") -AnnotationAssertion( "WBbt:0008074") -AnnotationAssertion( "syncitium") -AnnotationAssertion( "syncytial cell") -AnnotationAssertion( "syncytium") +AnnotationAssertion(Annotation( "FB:ma") Annotation( "Wikipedia:Multinucleate") "A cell with more than one nucleus.") +AnnotationAssertion(Annotation( "Wikipedia:Multinucleate") "multinucleated cells") +AnnotationAssertion(Annotation( "Wikipedia:Multinucleate") "polynuclear cells") AnnotationAssertion(rdfs:label "multinucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43775,10 +43538,23 @@ SubClassOf( ObjectSomeValuesFrom( (stratified squamous epithelial cell) +AnnotationAssertion(Annotation( "PMID:30422572") Annotation( "Wikipedia:Epithelium") Annotation( "Wikipedia:Stratified_squamous_epithelium") "A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stratified squamous epithelial cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (stratified cuboidal epithelial cell) + +AnnotationAssertion(Annotation( "PMID:30422572") Annotation( "Wikipedia:Stratified_cuboidal_epithelium") "A stratified epithelial cell that is part of cuboidal epithelium, characterized by multiple layers of cuboidal cells forming the apical layer. This provides a protective lining for ducts in large glands, such as sweat glands.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "stratified cuboidal epithelial cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Merkel cell) @@ -43795,7 +43571,7 @@ SubClassOf( ObjectSomeValuesFrom( (eukaryotic cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that only exists in Eukaryota.") +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that in taxon some Eukaryota.") AnnotationAssertion( "MESH:D005057") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eukaryotic cell") @@ -43809,6 +43585,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eye photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43924,16 +43701,22 @@ SubClassOf( ObjectSomeValuesFrom( (pulmonary alveolar epithelial cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:20054144") Annotation( "PMID:29463737") "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-09-02T08:27:21Z"^^xsd:dateTime) AnnotationAssertion( "BTO:0000395") AnnotationAssertion( "CALOHA:TS-2168") AnnotationAssertion( "FMA:62499") +AnnotationAssertion( "MESH:D056809") AnnotationAssertion( "alveolar epithelial cell") +AnnotationAssertion( "alveolus of lung epithelial cell") +AnnotationAssertion( "epithelial cell of alveolus of lung") AnnotationAssertion(Annotation( "PMID:32491474") "pneumocyte") AnnotationAssertion( "pneumonocyte") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary alveolar epithelial cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (stuff accumulating cell) @@ -44000,7 +43783,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "scleral cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44011,7 +43794,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "choroidal cell of the eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44022,17 +43805,17 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "extraembryonic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trophoblast cell) -AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "MESH:D014327") "A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface.") +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "MESH:D014327") Annotation( "PMID:37630754") Annotation( "doi:10.1007/978-3-030-84725-8") "An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development.") AnnotationAssertion( "FMA:83028") -AnnotationAssertion( "trophoblastic cell") +AnnotationAssertion(Annotation( "doi:10.1007/978-3-030-84725-8") "trophoblastic cell") AnnotationAssertion(rdfs:label "trophoblast cell") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epiblast cell) @@ -44267,6 +44050,7 @@ AnnotationAssertion(rdfs:label "dend EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44415,7 +44199,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stromal cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -44423,6 +44206,7 @@ SubClassOf( ObjectSomeValuesFrom( "MESH:D019864") "A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin.") AnnotationAssertion( "FMA:62935") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000502") AnnotationAssertion( "D cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "type D enteroendocrine cell") @@ -44452,7 +44236,7 @@ AnnotationAssertion(rdfs:label "type SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (gastrin secreting cell) @@ -44468,12 +44252,6 @@ AnnotationAssertion(Annotation( "androgen binding protein secreting cell") SubClassOf( ) -# Class: (paracrine cell) - -AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0198529171") "A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it.") -AnnotationAssertion(rdfs:label "paracrine cell") -SubClassOf( ) - # Class: (cardiac muscle myoblast) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "MESH:D032386") "A precursor cell destined to differentiate into cardiac muscle cell.") @@ -44530,8 +44308,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "syncytiotrophoblast cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (afferent neuron) @@ -44612,6 +44390,7 @@ AnnotationAssertion(rdfs:label "proe EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44640,6 +44419,7 @@ AnnotationAssertion(Annotation( "basophilic erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44657,6 +44437,7 @@ AnnotationAssertion(Annotation( "polychromatophilic erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44762,6 +44543,7 @@ SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44781,6 +44563,7 @@ AnnotationAssertion( "reticulocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44808,6 +44591,7 @@ AnnotationAssertion(rdfs:label "prom EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44824,7 +44608,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amacrine cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -44851,6 +44634,7 @@ AnnotationAssertion(rdfs:label "angi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -44891,6 +44675,7 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -45003,6 +44788,7 @@ AnnotationAssertion(rdfs:label "baso EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -45043,6 +44829,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "http://www.copewithcytokines.de") "A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).") AnnotationAssertion( "FMA:83625") AnnotationAssertion( "MESH:D061354") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000622") AnnotationAssertion( "acinic cell") AnnotationAssertion( "acinous cell") AnnotationAssertion( ) @@ -45150,6 +44937,7 @@ AnnotationAssertion(rdfs:label "hepa EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -45201,7 +44989,6 @@ AnnotationAssertion(Annotation( "PMID:34734454") "Sox2-positive stem cell") AnnotationAssertion(Annotation( "PMID:18287078") Annotation( "PMID:31620083") Annotation( "PMID:34734454") Annotation( "doi:10.23937/2572-407X.1510006") rdfs:comment "Folliculostellate cells are a heterogeneous group of cells rather than a single cell type, with different morphology and gene expression profiles. Due to this heterogeneity, it is unclear if different properties that have been attributed to folliculostellate cells (pluripotent, proliferative, phagocytic) are common in all folliculostellate cells or limited to particular subsets.") AnnotationAssertion(rdfs:label "folliculostellate cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -45238,7 +45025,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Do all of these cells really develop from some mesenchymal stem cell?") AnnotationAssertion(rdfs:label "mesangial cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -45288,6 +45074,7 @@ AnnotationAssertion( "primary spermatocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -45300,6 +45087,7 @@ AnnotationAssertion( "secondary spermatocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -45307,6 +45095,7 @@ SubClassOf( ObjectSomeValuesFrom( (fenestrated endothelial cell) AnnotationAssertion(Annotation( "DOI:10.1007/978-3-211-99390-3_133") "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000666") AnnotationAssertion( "window cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fenestrated endothelial cell") @@ -45372,8 +45161,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "muscle precursor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -45393,6 +45182,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "JB:jb") Annotation( "PMID:15153415") "A cell that stores and secretes pancreatic polypeptide hormone.") AnnotationAssertion( "FMA:62938") AnnotationAssertion( "FMA:83409") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000696") AnnotationAssertion( "type F enteroendocrine cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "PP cell") @@ -45458,7 +45248,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "leukocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -45570,7 +45359,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myeloid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -45793,6 +45582,7 @@ AnnotationAssertion( "alpha-beta T cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -45877,6 +45667,7 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "gamma-delta T cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (immature gamma-delta T cell) @@ -45918,6 +45709,7 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "immature single positive thymocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -45942,6 +45734,7 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "DN2 thymocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -45964,6 +45757,7 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "DN3 thymocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -45985,6 +45779,7 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "DN4 thymocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46242,6 +46037,7 @@ AnnotationAssertion(rdfs:comment "Mo AnnotationAssertion(rdfs:label "pro-NK cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46269,6 +46065,7 @@ AnnotationAssertion(rdfs:comment "Hu AnnotationAssertion(rdfs:label "pro-B cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46322,6 +46119,7 @@ AnnotationAssertion(rdfs:label "mast EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46376,8 +46174,9 @@ AnnotationAssertion( "Markers differ between mouse and human.") AnnotationAssertion(rdfs:label "hematopoietic multipotent progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46523,6 +46322,7 @@ SubClassOf( (classical monocyte) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GO_REF:0000031") Annotation( "PMID:16322748") Annotation( "PMID:18303997") Annotation( "PMID:20628149") Annotation( "PMID:20870168") "A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000860") AnnotationAssertion( "inflammatory monocyte") AnnotationAssertion( ) AnnotationAssertion( ) @@ -46530,6 +46330,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "classical monocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46549,6 +46350,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "elicited macrophage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46596,6 +46398,7 @@ AnnotationAssertion(rdfs:label "peri EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46609,6 +46412,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "myeloid suppressor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46656,6 +46460,7 @@ AnnotationAssertion( "DN1 thymic pro-T cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -46947,6 +46752,7 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "pre-natural killer cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47422,6 +47228,7 @@ AnnotationAssertion(rdfs:comment "Ce AnnotationAssertion(rdfs:label "Kit and Sca1-positive hematopoietic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47457,6 +47264,7 @@ AnnotationAssertion(rdfs:label "CD34 EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47473,6 +47281,7 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47504,6 +47313,7 @@ AnnotationAssertion(rdfs:comment "Ce AnnotationAssertion(rdfs:label "CD34-positive, CD38-negative hematopoietic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47524,6 +47334,7 @@ AnnotationAssertion(rdfs:label "Kit- EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47559,6 +47370,7 @@ AnnotationAssertion(rdfs:label "CD7- EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47572,6 +47384,7 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "CD7-positive lymphoid progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47589,6 +47402,7 @@ AnnotationAssertion(rdfs:label "comm EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47653,7 +47467,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (effector CD4-positive, alpha-beta T cell) @@ -47709,6 +47523,7 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "CD14-positive monocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47742,6 +47557,7 @@ AnnotationAssertion(rdfs:label "comm EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47859,6 +47675,7 @@ AnnotationAssertion( "erythroid progenitor cell, mammalian") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47901,6 +47718,7 @@ AnnotationAssertion( "Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex).") AnnotationAssertion(rdfs:label "lymphocyte of B lineage, CD19-positive") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -47914,6 +47732,7 @@ AnnotationAssertion( "CD19+ B cell") AnnotationAssertion( "CD19-positive B cell") AnnotationAssertion(rdfs:label "B cell, CD19-positive") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -48037,6 +47856,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48051,6 +47871,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48084,6 +47905,7 @@ AnnotationAssertion(rdfs:label "pre- EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48112,6 +47934,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "Kit-positive macrophage dendritic cell progenitor") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48199,6 +48022,7 @@ AnnotationAssertion(rdfs:comment "Ce AnnotationAssertion(rdfs:label "Kit-negative, Ly-76 high orthochromatophilic erythroblasts") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48215,6 +48039,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "CD71-negative, GlyA-positive orthochromatic erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48252,6 +48077,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "GlyA-positive erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48264,6 +48090,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "Ly-76 high positive erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48276,6 +48103,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "Kit-positive megakaryocyte progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48294,6 +48122,7 @@ AnnotationAssertion(rdfs:comment "Ma AnnotationAssertion(rdfs:label "CD9-positive, CD41-positive megakaryocyte cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48310,6 +48139,7 @@ AnnotationAssertion(rdfs:label "baso EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48354,7 +48184,7 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hematopoietic lineage restricted progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48369,7 +48199,7 @@ AnnotationAssertion( "This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060).") AnnotationAssertion(rdfs:label "hematopoietic oligopotent progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -48665,6 +48495,7 @@ AnnotationAssertion( AnnotationAssertion( "BTO:0000028") AnnotationAssertion( "CALOHA:TS-0737") AnnotationAssertion( "FMA:63032") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002064") AnnotationAssertion( "acinar cell of pancreas") AnnotationAssertion( ) AnnotationAssertion( ) @@ -48681,6 +48512,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-09-10T10:48:54Z"^^xsd:dateTime) AnnotationAssertion( "FMA:62939") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002067") AnnotationAssertion(rdfs:label "type A enteroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -48741,7 +48573,6 @@ AnnotationAssertion( AnnotationAssertion( "FMA:69075") AnnotationAssertion(rdfs:label "endo-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -48753,7 +48584,6 @@ AnnotationAssertion( AnnotationAssertion( "FMA:69074") AnnotationAssertion(rdfs:label "ecto-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -48766,7 +48596,6 @@ AnnotationAssertion( "epithelial mesenchymal cell") AnnotationAssertion(rdfs:label "meso-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -49290,12 +49119,14 @@ SubClassOf( ObjectSomeValuesFrom( (ciliated columnar cell of tracheobronchial tree) -AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0517223651") "A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree.") +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:28400610") "A multi-ciliated epithelial cell located in the trachea and bronchi, characterized by a columnar shape and motile cilia on its apical surface. These cilia facilitate mucociliary clearance by moving mucus and trapped particles toward the pharynx.") AnnotationAssertion( ) AnnotationAssertion( "2010-08-24T03:38:29Z"^^xsd:dateTime) AnnotationAssertion( "FMA:70542") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002145") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) Annotation( "PMID:25386990") rdfs:comment "These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles.") AnnotationAssertion(rdfs:label "ciliated columnar cell of tracheobronchial tree") SubClassOf( ) SubClassOf( ) @@ -49317,15 +49148,27 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell of uterus) -AnnotationAssertion(Annotation( "GOC:tfm") "An epithelial cell of the uterus.") +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:11331626") Annotation( "PMID:16960017") Annotation( "PMID:21698266") "An epithelial cell of the uterus. This cell has a mesodermal origin.") AnnotationAssertion( ) AnnotationAssertion( "2010-08-24T10:45:54Z"^^xsd:dateTime) AnnotationAssertion( "FMA:256161") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of uterus") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (columnar cell of endocervix) + +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") Annotation( "doi:/10.1016/j.autneu.2015.04.008") "A simple columnar epithelial cell located in the endocervix.") +AnnotationAssertion( ) +AnnotationAssertion( "2010-08-24T10:47:47Z"^^xsd:dateTime) +AnnotationAssertion( "FMA:86486") +AnnotationAssertion(rdfs:label "columnar cell of endocervix") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (corneocyte) @@ -49336,8 +49179,8 @@ AnnotationAssertion( "FMA:68650") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "corneocyte") -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -49415,14 +49258,14 @@ SubClassOf( ObjectSomeValuesFrom( (mucous cell of stomach) -AnnotationAssertion(Annotation( "GOC:tfm") "A mucous cell in the epithelium of the stomach.") +AnnotationAssertion(Annotation( "GOC:tfm") "An epithelial cell of the stomach. This cell produces mucous.") AnnotationAssertion( ) AnnotationAssertion( "2010-08-25T03:38:51Z"^^xsd:dateTime) AnnotationAssertion( "FMA:63464") AnnotationAssertion(rdfs:label "mucous cell of stomach") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (stem cell of gastric gland) @@ -49433,8 +49276,7 @@ AnnotationAssertion( "stem cell of gastric gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (basal cell of epidermis) @@ -49453,18 +49295,21 @@ SubClassOf( (glomerular endothelial cell) -AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:15840009") "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate.") +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:15840009") "An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate.") AnnotationAssertion( ) AnnotationAssertion( "2010-08-26T10:59:44Z"^^xsd:dateTime) AnnotationAssertion( "BTO:0004632") AnnotationAssertion( "FMA:70970") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(Annotation( "PMID:18480313") Annotation( "PMID:19129259") Annotation( "PMID:33123011") rdfs:comment "Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes.") AnnotationAssertion(rdfs:label "glomerular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (granulocytopoietic cell) @@ -49694,6 +49539,18 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (squamous cell of ectocervix) + +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:32644501") Annotation( "doi:/10.1016/j.autneu.2015.04.008") Annotation( "http://www.bu.edu/histology/p/19404loa.htm") "A stratified squamous epithelial cell located in the ectocervix.") +AnnotationAssertion( ) +AnnotationAssertion( "2010-09-08T09:12:23Z"^^xsd:dateTime) +AnnotationAssertion( "FMA:86483") +AnnotationAssertion( "ectocervical squamous cell") +AnnotationAssertion(rdfs:label "squamous cell of ectocervix") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (peripheral blood stem cell) AnnotationAssertion(Annotation( "GOC:tfm") "A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells).") @@ -49905,6 +49762,7 @@ AnnotationAssertion( AnnotationAssertion( "BTO:0000805") AnnotationAssertion( "FMA:70588") AnnotationAssertion( "MESH:D050418") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002275") AnnotationAssertion( "PP cell of pancreatic islet") AnnotationAssertion( "PP-cell of pancreatic islet") AnnotationAssertion( "pancreatic polypeptide-secreting cell") @@ -49997,7 +49855,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (connective tissue cell) @@ -50011,7 +49869,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "connective tissue cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic cell (metazoa)) @@ -50071,7 +49929,6 @@ AnnotationAssertion(Annotation( "FMA:73280") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "luminal epithelial cell of mammary gland") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -50107,6 +49964,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury.") AnnotationAssertion( ) AnnotationAssertion( "2010-09-20T02:10:36Z"^^xsd:dateTime) +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002329") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "basal epithelial cell of tracheobronchial tree") @@ -50120,7 +49978,7 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ciliated cell of the bronchus") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -50207,6 +50065,7 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "fetal liver hematopoietic progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -50226,6 +50085,7 @@ AnnotationAssertion( "yolk sac hematopoietic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -50328,6 +50188,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "ISBN:0721662544") "A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion.") AnnotationAssertion( ) AnnotationAssertion( "2010-09-23T04:42:27Z"^^xsd:dateTime) +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002370") AnnotationAssertion(Annotation( "MP:0010863") "respiratory mucosa goblet cells") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "respiratory goblet cell") @@ -50337,15 +50198,15 @@ SubClassOf( (myotube) -AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:tfm") Annotation( "ISBN:0323052908") Annotation( "PMID:22274696") "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts.") +AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:tfm") Annotation( "ISBN:0323052908") Annotation( "PMID:22274696") "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development.") AnnotationAssertion( ) AnnotationAssertion( "2010-09-24T01:13:01Z"^^xsd:dateTime) -AnnotationAssertion( "myotubule") -AnnotationAssertion( "single cell sarcomere") +AnnotationAssertion(Annotation( "FBbt:00005812") "myofiber") +AnnotationAssertion(Annotation( "FBbt:00005812") "myofibril") AnnotationAssertion(rdfs:label "myotube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (intermediate monocyte) @@ -50462,6 +50323,7 @@ AnnotationAssertion( "mature T cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -50540,6 +50402,7 @@ AnnotationAssertion(rdfs:comment "ET AnnotationAssertion(rdfs:label "early T lineage precursor") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -50714,7 +50577,6 @@ AnnotationAssertion(Annotation( "PMID:11756508") Annotation( ) "O2A/OPC") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "ISBN:9780702028991") Annotation( "PMID:10704434") Annotation( "PMID:2182078") rdfs:comment "This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991).") AnnotationAssertion(rdfs:label "oligodendrocyte precursor cell") SubClassOf( ) SubClassOf( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -50876,6 +50738,7 @@ AnnotationAssertion(rdfs:label "bone EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -50890,6 +50753,7 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "adipose macrophage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -50946,6 +50810,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "MP:0004381") "A melanocyte that produces pigment within the hair follicle.") AnnotationAssertion( ) AnnotationAssertion( "2010-12-03T03:17:09Z"^^xsd:dateTime) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hair follicle melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -51012,7 +50877,7 @@ AnnotationAssertion( "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart.") AnnotationAssertion(rdfs:label "cardiocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (adventitial cell) @@ -51097,7 +50962,7 @@ AnnotationAssertion(Annotation( "GOC:tfm") "uterine cervix epithelial cell") AnnotationAssertion(rdfs:label "epithelial cell of cervix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of amnion) @@ -51128,6 +50993,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "PMID:23720296") "An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes.") AnnotationAssertion( ) AnnotationAssertion( "2011-02-28T01:20:20Z"^^xsd:dateTime) +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002538") AnnotationAssertion(Annotation( "PMID:23720296") "small bile duct cholangiocyte") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intrahepatic cholangiocyte") @@ -51174,6 +51040,7 @@ AnnotationAssertion( "2011-02-28T03:48:11Z"^^xsd:dateTime) AnnotationAssertion( "FMA:62104") AnnotationAssertion( "KUPO:0001099") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002543") AnnotationAssertion( "endothelial cell of vein") AnnotationAssertion( "venous endothelial cell") AnnotationAssertion( ) @@ -51183,15 +51050,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (embryonic blood vessel endothelial progenitor cell) - -AnnotationAssertion(Annotation( "GOC:tfm") "An endothelial progenitor cell that participates in angiogenesis during development.") -AnnotationAssertion( ) -AnnotationAssertion( "2011-02-28T04:20:39Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "See CL:0002619.") -AnnotationAssertion(rdfs:label "embryonic blood vessel endothelial progenitor cell") -SubClassOf( ) - # Class: (fibroblast of the aortic adventitia) AnnotationAssertion(Annotation( "GOC:tfm") "A fibroblast of the aortic adventitia.") @@ -51318,7 +51176,7 @@ AnnotationAssertion( "2011-03-01T04:11:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "hair follicle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (intestinal epithelial cell) @@ -51358,6 +51216,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "A mesenchymal stem cell of adipose tissue.") AnnotationAssertion( ) AnnotationAssertion( "2011-03-01T09:57:17Z"^^xsd:dateTime) +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002570") AnnotationAssertion( "mesenchymal stem cell of adipose") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchymal stem cell of adipose tissue") @@ -51433,6 +51292,7 @@ SubClassOf( "GOC:tfm") "A blood vessel endothelial cell that is part of the retina.") AnnotationAssertion( ) AnnotationAssertion( "2011-03-06T03:28:27Z"^^xsd:dateTime) +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002585") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -51449,6 +51309,7 @@ AnnotationAssertion( "2011-03-06T03:37:09Z"^^xsd:dateTime) AnnotationAssertion( "BTO:0004910") AnnotationAssertion( "FMA:75802") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002586") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -51641,7 +51502,7 @@ SubClassOf( (astrocyte of the cerebral cortex) -AnnotationAssertion(Annotation( "GOC:tfm") "An astrocyte of the cerebral cortex.") +AnnotationAssertion(Annotation( "GOC:tfm") "A transcriptomically distinct astrocyte that is found in the cerebral cortex.") AnnotationAssertion( ) AnnotationAssertion( "2011-03-06T06:57:36Z"^^xsd:dateTime) AnnotationAssertion( ) @@ -51760,7 +51621,7 @@ AnnotationAssertion( "2011-03-14T12:46:28Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "gingival epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (prostate stromal cell) @@ -51823,6 +51684,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "PMID:20699479") "A basal cell in the respiratory tract.") AnnotationAssertion( ) AnnotationAssertion( "2011-06-21T03:11:10Z"^^xsd:dateTime) +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002633") AnnotationAssertion( "airway basal cell") AnnotationAssertion( "airway basal stem cell") AnnotationAssertion( ) @@ -51867,9 +51729,10 @@ AnnotationAssertion( "2011-07-08T03:54:08Z"^^xsd:dateTime) AnnotationAssertion( "FMA:86489") AnnotationAssertion(rdfs:label "glandular cell of endometrium") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glandular cell of esophagus) @@ -51894,14 +51757,15 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (glandular cell of stomach) +# Class: (glandular epithelial cell of stomach) AnnotationAssertion(Annotation( "GOC:tfm") "A glandular epithelial cell that is part of the stomach.") AnnotationAssertion( ) AnnotationAssertion( "2011-07-11T01:20:35Z"^^xsd:dateTime) AnnotationAssertion( "CALOHA:TS-1284") AnnotationAssertion( "FMA:86554") -AnnotationAssertion(rdfs:label "glandular cell of stomach") +AnnotationAssertion( "glandular cell of stomach") +AnnotationAssertion(rdfs:label "glandular epithelial cell of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -51923,7 +51787,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2011-08-16T02:38:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "retinal progenitor cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -51969,6 +51832,7 @@ AnnotationAssertion( "natural helper lymphocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -52012,6 +51876,7 @@ SubClassOf( ObjectSomeValuesFrom( (renal principal cell) AnnotationAssertion(Annotation( "CL:CVS") "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005009") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal principal cell") SubClassOf( ) @@ -52019,14 +51884,20 @@ SubClassOf( (multi-ciliated epithelial cell) -AnnotationAssertion(Annotation( "CL:CVS") "A ciliated epithelial cell with many cilia.") +AnnotationAssertion(Annotation( "CL:CVS") Annotation( "PMID:28400610") Annotation( "PMID:30422572") Annotation( "PMID:38032388") "A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface.") AnnotationAssertion( "multi-ciliated cell"@en) AnnotationAssertion( "multiciliated cell"@en) +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005012") AnnotationAssertion( "multiciliated epithelial cell"@en) AnnotationAssertion(Annotation( ) "MCC"@en) AnnotationAssertion( ) +AnnotationAssertion(Annotation( "PMID:22118931") Annotation( "PMID:23959957") Annotation( "PMID:25729351") Annotation( "PMID:26378583") rdfs:comment "While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility") AnnotationAssertion(rdfs:label "multi-ciliated epithelial cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphangioblast) @@ -52065,6 +51936,7 @@ SubClassOf( ObjectSomeValuesFrom( (hepatoblast) AnnotationAssertion(Annotation( "GOC:CVS") Annotation( "PMID:18356246") Annotation( "PMID:20483998") Annotation( "PMID:26798363") Annotation( "https://orcid.org/0000-0003-1940-6740") "Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005026") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hepatoblast"@en) SubClassOf( ) @@ -52076,8 +51948,8 @@ AnnotationAssertion( "2012-06-15T01:27:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "unsure of neural crest contribution. In VSAO we have develops_from CL:0000008") AnnotationAssertion(rdfs:label "preameloblast") -SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -52099,6 +51971,7 @@ AnnotationAssertion( "2012-06-15T04:37:13Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "precementoblast") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (preodontoblast) @@ -52118,7 +51991,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2012-06-27T08:27:35Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "premigratory neural crest cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -52211,6 +52083,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchymal cell") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -52305,6 +52178,16 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (salivary gland cell) + +AnnotationAssertion( "Any cell in a salivary gland.") +AnnotationAssertion( "GOC:pr") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Salivary_gland") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "salivary gland cell") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (enteroendocrine cell of small intestine) AnnotationAssertion(Annotation( "http://orcid.org/0000-0003-3440-1876") "An enteroendocrine cell that is located in the small intestine.") @@ -52418,8 +52301,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "colon goblet cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (stromal cell of lamina propria of colon) @@ -52598,7 +52481,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of endometrial gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell of respiratory system lymphatic vessel) @@ -52758,19 +52641,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (epithelial cell of alveolus of lung) - -AnnotationAssertion( "An epithelial cell that is part_of a alveolus of lung.") -AnnotationAssertion( ) -AnnotationAssertion( "MESH:D056809") -AnnotationAssertion( "alveolus of lung epithelial cell") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "May be merged with pneumocyte in future") -AnnotationAssertion(rdfs:label "epithelial cell of alveolus of lung") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (mononuclear cell of bone marrow) AnnotationAssertion( "A mononuclear cell that is part_of a bone marrow.") @@ -52806,7 +52676,6 @@ AnnotationAssertion(Annotation( "camera type eye photoreceptor cell") AnnotationAssertion(rdfs:label "camera-type eye photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -52904,6 +52773,7 @@ SubClassOf( ObjectSomeValuesFrom( (neural crest cell) AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-5208-3432") Annotation( "https://orcid.org/0000-0002-9900-7880") "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0011012") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural crest cell") SubClassOf( ) @@ -52986,7 +52856,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -53143,6 +53013,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tracheobronchial serous cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -53297,12 +53168,12 @@ SubClassOf( ObjectSomeValuesFrom( (lung goblet cell) AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any goblet cell that is part of some lung epithelium.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000143") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung goblet cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (cardiac valve cell) @@ -53326,6 +53197,7 @@ SubClassOf( (lung neuroendocrine cell) AnnotationAssertion(Annotation( "PMID:33355253") Annotation( "doi:10.3109/01902148209069653") Annotation( "doi:10.7554/eLife.78216") "A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000223") AnnotationAssertion(Annotation( "PMID:33355253") "pulmonary neuroendocrine cell") AnnotationAssertion(Annotation( "PMID:33355253") Annotation( ) "PNEC") AnnotationAssertion( ) @@ -53343,13 +53215,14 @@ SubClassOf( ObjectSomeValuesFrom( (lung ciliated cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any ciliated cell that is part of some lung.") +AnnotationAssertion(Annotation( "PMID:27864314") "An epithelial cell that is part of the lung epithelium. This cell is characterised by the presence of cilia on its apical surface.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung ciliated cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung secretory cell) @@ -53358,6 +53231,7 @@ AnnotationAssertion( "lung secretory cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (trophectodermal cell) @@ -53587,7 +53461,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "large intestine goblet cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -53601,7 +53475,7 @@ AnnotationAssertion(rdfs:label "panc EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pyloric gastric gland goblet cell) @@ -53624,7 +53498,7 @@ AnnotationAssertion( "duodenal goblet cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (jejunal goblet cell) @@ -53841,6 +53715,7 @@ AnnotationAssertion(Annotation( "BTO:0004758") AnnotationAssertion( "FMA:67761") AnnotationAssertion( "KUPO:0001095") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000413") AnnotationAssertion( "arterial endothelial cell") AnnotationAssertion( ) AnnotationAssertion( ) @@ -53937,6 +53812,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "An epithelial cell that is part of the lacrimal sac.") AnnotationAssertion( "FMA:70560") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000436") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of lacrimal sac") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -54024,6 +53900,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "An epithelial cell that is part of the collecting duct of renal tubule.") AnnotationAssertion( "FMA:70982") AnnotationAssertion( "KUPO:0001059") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000454") AnnotationAssertion(Annotation( "FMA:70982") "epithelial cell of renal collecting tubule") AnnotationAssertion( ) AnnotationAssertion( ) @@ -54138,11 +54015,11 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "PMID:16550043") Annotation( "PMID:18356246") "An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts.") AnnotationAssertion( "FMA:86481") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000488") AnnotationAssertion( "epithelial cell of bile duct") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cholangiocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -54162,6 +54039,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "A mesothelial cell that is part of the pleura.") AnnotationAssertion( "FMA:86737") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000491") AnnotationAssertion(Annotation( "FMA:86737") "pleural mesothelial cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell of pleura") @@ -54182,6 +54060,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "A mesothelial cell that is part of the visceral pleura.") AnnotationAssertion( "FMA:86739") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000493") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell of visceral pleura") @@ -54213,8 +54092,9 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "small intestine goblet cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney cell) @@ -54223,7 +54103,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney interstitial cell) @@ -54314,7 +54194,7 @@ AnnotationAssertion(Annotation( "KUPO:0001115") AnnotationAssertion(rdfs:label "lower urinary tract cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ureteral cell) @@ -54323,7 +54203,7 @@ AnnotationAssertion(Annotation( "KUPO:0001116") AnnotationAssertion(rdfs:label "ureteral cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney nerve cell) @@ -54332,7 +54212,6 @@ AnnotationAssertion(Annotation( "KUPO:0001015") AnnotationAssertion(rdfs:label "kidney nerve cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -54455,7 +54334,6 @@ AnnotationAssertion(Annotation( "KUPO:0001014") AnnotationAssertion(rdfs:label "kidney blood vessel cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -54472,13 +54350,13 @@ SubClassOf( ObjectSomeValuesFrom( (kidney capillary endothelial cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any kidney blood vessel cell that is part of some kidney capillary.") +AnnotationAssertion( "An endothelial cell that is part of the capillary of the kidney.") AnnotationAssertion( "KUPO:0001030") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney capillary endothelial cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -54505,20 +54383,20 @@ SubClassOf( ObjectSomeValuesFrom( (glomerular capillary endothelial cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any kidney capillary endothelial cell that is part of some glomerular capillary endothelium.") +AnnotationAssertion( "An endothelial cell that is part of the glomerular capillary of the kidney.") AnnotationAssertion( "KUPO:0001037") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001005") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "glomerular capillary endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney afferent arteriole cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any kidney arterial blood vessel cell that is part of some renal afferent arteriole.") +AnnotationAssertion(Annotation( "PMID:16990493") Annotation( "PMID:22733355") Annotation( "PMID:24066938") Annotation( "PMID:25834230") "An endothelial cell which is part of the afferent arteriole in the kidney. This cell is responsible for maintaining renal blood flow and glomerular filtration rate.") AnnotationAssertion( "KUPO:0001038") AnnotationAssertion(rdfs:label "kidney afferent arteriole cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -54565,8 +54443,9 @@ SubClassOf( (kidney afferent arteriole endothelial cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any endothelial cell that is part of some renal afferent arteriole.") +AnnotationAssertion(Annotation( "PMID:16990493") Annotation( "PMID:22733355") Annotation( "PMID:24066938") Annotation( "PMID:25834230") "An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration.") AnnotationAssertion( "KUPO:0001039") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001096") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney afferent arteriole endothelial cell") @@ -54577,7 +54456,7 @@ SubClassOf( (kidney afferent arteriole smooth muscle cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any smooth muscle cell that is part of some renal afferent arteriole.") +AnnotationAssertion(Annotation( "PMID:16990493") Annotation( "PMID:22733355") Annotation( "PMID:24066938") Annotation( "PMID:25834230") "A smooth muscle cell found in the wall of the afferent arteriole. This cell contracts and relaxes in response to changes in blood pressure, a process known as a myogenic response, to alter artery diameter and regulate blood flow into the glomeruli.") AnnotationAssertion( "KUPO:0001040") AnnotationAssertion(rdfs:label "kidney afferent arteriole smooth muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -54685,6 +54564,7 @@ SubClassOf( ObjectSomeValuesFrom( "FBC:Autogenerated") "Any renal principal cell that is part of some collecting duct of renal tubule.") AnnotationAssertion( "KUPO:0001128") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001431") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney collecting duct principal cell") @@ -54709,7 +54589,6 @@ SubClassOf( ObjectSomeValuesFrom( "PMID:18603310") "A neuron residing in the olfactory bulb that serve to process and refine signals arising from olfactory sensory neurons") AnnotationAssertion(rdfs:label "olfactory bulb interneuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -54726,7 +54605,6 @@ SubClassOf( ObjectSomeValuesFrom( "MP:0009955") "The principal glutaminergic neuron located in the outer third of the external plexiform layer of the olfactory bulb; a single short primary dendrite traverses the outer external plexiform layer and terminates within an olfactory glomerulus in a tuft of branches, where it receives the input from olfactory receptor neuron axon terminals; axons of the tufted cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, olfactory tubercle, and amygdala.") AnnotationAssertion(rdfs:label "olfactory bulb tufted cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -55009,12 +54887,14 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (seminal vesicle glandular cell) AnnotationAssertion(Annotation( "NPX:PDR") "Glandular cell of seminal vesicle epithelium.") AnnotationAssertion( "CALOHA:TS-1283") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001597") AnnotationAssertion(Annotation( "CALOHA:TS-1283") "seminal vesicle glandular cells") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "seminal vesicle glandular cell") @@ -55066,7 +54946,7 @@ SubClassOf( ObjectSomeValuesFrom( (cerebral cortex endothelial cell) -AnnotationAssertion(Annotation( "NPX:PDR") "Endothelial cells forming the walls of the capillaries within the cerebral cortex.") +AnnotationAssertion(Annotation( "NPX:PDR") "A distinct endothelial cell forming the walls of the capillaries within the cerebral cortex.") AnnotationAssertion( "CALOHA:TS-2372") AnnotationAssertion(Annotation( "CALOHA:TS-2372") "cerebral cortex endothelial cells") AnnotationAssertion(Annotation( "CALOHA:TS-2372") "endothelial cells of cerebral cortex") @@ -55360,7 +55240,7 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000020") AnnotationAssertion(rdfs:label "inner cell mass cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sebaceous gland cell) @@ -55372,7 +55252,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sebaceous gland cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac septum cell) @@ -55642,6 +55522,19 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (placental villus capillary endothelial cell) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any capillary endothelial cell that is part of a placenta.") +AnnotationAssertion( ) +AnnotationAssertion( "2014-10-07T17:55:56Z"^^xsd:dateTime) +AnnotationAssertion( "CL:2000062") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "http://www.ncbi.nlm.nih.gov/books/NBK53245/") +AnnotationAssertion(rdfs:label "placental villus capillary endothelial cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (ovarian fibroblast) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any fibroblast that is part of a female gonad.") @@ -56134,7 +56027,7 @@ AnnotationAssertion(Annotation( "2022-11-30T14:35:08Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "interstitial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (valve interstitial cell) @@ -56185,20 +56078,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (endometrial ciliated epithelial cell) - -AnnotationAssertion(Annotation( "doi:10.1038/s41591-020-1040-z") Annotation( "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") "A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium.") -AnnotationAssertion( "2023-02-09T11:25:14Z"^^xsd:dateTime) -AnnotationAssertion( "ciliated cell of the uterus") -AnnotationAssertion( "uterine ciliated cell") -AnnotationAssertion( "ciliated cell of the endometrium") -AnnotationAssertion( "endometrium ciliated epithelial cell") -AnnotationAssertion(Annotation( "ttps://www.nature.com/articles/s41591-020-1040-z") rdfs:comment "In human samples, the expression of FOXJ1 protein, a regulator for motile cilia with epithelial lineage identity, has been noted.") -AnnotationAssertion(rdfs:label "endometrial ciliated epithelial cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (TCR-positive macrophage) AnnotationAssertion(Annotation( ) Annotation( "PMID:26074923") "A macrophage that expresses the T cell receptor complex at the cell surface.") @@ -56210,6 +56089,7 @@ AnnotationAssertion(Annotation( "TCR-positive macrophage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ureteric bud cell) @@ -56220,7 +56100,6 @@ AnnotationAssertion( "PMID:24183650") Annotation( ) "UB cell") AnnotationAssertion(rdfs:label "ureteric bud cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -56475,6 +56354,31 @@ AnnotationAssertion(Annotation( "border associated macrophage"@en) SubClassOf( ) +# Class: (syncytial cell) + +AnnotationAssertion(Annotation( "PMID:20851884") Annotation( "Wikipedia:Syncytium") "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-15T10:38:46Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "WBbt:0008074") "syncytium") +AnnotationAssertion(Annotation( "PMID:9067520") Annotation( ) "SC") +AnnotationAssertion(rdfs:label "syncytial cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (intestinal villus capillary endothelial cell) + +AnnotationAssertion(Annotation( "PMID:18480313") Annotation( "PMID:35810168") Annotation( "PMID:38051275") "A capillary endothelial cell that is part of the intestinal villus. This cell is highly fenestrated, with fenestrations most numerous at the villus tips, and plays a vital role in nutrient absorption and maintaining the selective permeability of the intestinal barrier.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-09-17T10:03:25Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "PMID:35810168") "villus blood capillary endothelial cells") +AnnotationAssertion(Annotation( "PMID:38051275") "villus tip endothelial cell") +AnnotationAssertion(rdfs:label "intestinal villus capillary endothelial cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (mitochondrial genome maintenance) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:vw") "The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.") @@ -56528,7 +56432,6 @@ AnnotationAssertion( "sulfur amino acid metabolic process") SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (microtubule cytoskeleton organization) @@ -56639,9 +56542,20 @@ AnnotationAssertion( "lytic vacuole") SubClassOf( ) +# Class: (syncytium formation by plasma membrane fusion) + +AnnotationAssertion(Annotation( "GOC:mtg_muscle") Annotation( "GOC:tb") "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.") +AnnotationAssertion( "cell fusion") +AnnotationAssertion( "GO:0000768") +AnnotationAssertion(rdfs:label "syncytium formation by plasma membrane fusion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (chromatin) AnnotationAssertion(Annotation( "GOC:elh") Annotation( "PMID:20404130") "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28301"^^xsd:anyURI) AnnotationAssertion( "GO:0000789") AnnotationAssertion( "GO:0000790") AnnotationAssertion( "GO:0005717") @@ -56652,7 +56566,7 @@ AnnotationAssertion( "GO:0000785") AnnotationAssertion(rdfs:comment "Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.") AnnotationAssertion(rdfs:label "chromatin") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (euchromatin) @@ -56858,6 +56772,15 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (formation of translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:hjd") "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).") +AnnotationAssertion( "translation initiation ternary complex assembly") +AnnotationAssertion( "GO:0001677") +AnnotationAssertion(rdfs:label "formation of translation initiation ternary complex") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (gastric acid secretion) AnnotationAssertion(Annotation( "GOC:hjd") "The regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion.") @@ -57036,7 +56959,7 @@ SubClassOf( ObjectSomeValuesFrom( (serotonin secretion) -AnnotationAssertion(Annotation( "GOC:ef") Annotation( "ISBN:0198506732") Annotation( "ISBN:0781735149") "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.") +AnnotationAssertion(Annotation( "GOC:ef") Annotation( "ISBN:0198506732") Annotation( "ISBN:0781735149") "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesized in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.") AnnotationAssertion( "5-HT secretion") AnnotationAssertion( "5-hydroxytryptamine secretion") AnnotationAssertion(Annotation( "GOC:tb") "serotonin release") @@ -57286,7 +57209,7 @@ AnnotationAssertion(Annotation( "renal blood volume control of blood pressure") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "renal regulation of blood volume") AnnotationAssertion( "GO:0001977") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "renal system process involved in regulation of blood volume") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -58101,14 +58024,16 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (arachidonic acid metabolite production involved in inflammatory response) +# Class: (arachidonate metabolite production involved in inflammatory response) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") "The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28648"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:mah") "arachidonic acid metabolite production involved in acute inflammatory response") AnnotationAssertion( "production of arachidonic acid metabolites involved in acute inflammatory response") +AnnotationAssertion( "arachidonic acid metabolite production involved in inflammatory response") AnnotationAssertion( "production of arachidonic acid metabolites involved in inflammatory response") AnnotationAssertion( "GO:0002538") -AnnotationAssertion(rdfs:label "arachidonic acid metabolite production involved in inflammatory response") +AnnotationAssertion(rdfs:label "arachidonate metabolite production involved in inflammatory response") SubClassOf( ) # Class: (prostaglandin production involved in inflammatory response) @@ -59907,7 +59832,7 @@ AnnotationAssertion(Annotation(rdfs:label "(S)-Hydroxybutanoyl-CoA+NAD<=>Acetoac AnnotationAssertion(Annotation(rdfs:label "(S)-Hydroxyhexanoyl-CoA+NAD<=>3-Oxohexanoyl-CoA+NADH+H") "Reactome:R-HSA-77323") AnnotationAssertion(Annotation(rdfs:label "(S)-Hydroxyoctanoyl-CoA+NAD<=>3-Oxooctanoyl-CoA+NADH+H") "Reactome:R-HSA-77331") AnnotationAssertion(Annotation(rdfs:label "(S)-Hydroxydecanoyl-CoA+NAD<=>3-Oxodecanoyl-CoA+NADH+H") "Reactome:R-HSA-77342") -AnnotationAssertion( "UM-BBD_enzymeID:e0664") +AnnotationAssertion( "UM-BBD_reactionID:r1063") AnnotationAssertion(Annotation( "EC:1.1.1.35") "beta-hydroxybutyrylcoenzyme A dehydrogenase activity") AnnotationAssertion(Annotation( "PMID:19685079") "3-oxoacyl-thioester reductase activity") AnnotationAssertion(Annotation( "EC:1.1.1.35") "L-3-hydroxyacyl CoA dehydrogenase activity") @@ -59923,7 +59848,7 @@ SubClassOf( (alkaline phosphatase activity) -AnnotationAssertion(Annotation( "EC:3.1.3.1") Annotation( "RHEA:15017") "Catalysis of the reaction: a phosphate monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.") +AnnotationAssertion(Annotation( "EC:3.1.3.1") "Catalysis of the reaction: a phosphate monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.") AnnotationAssertion(Annotation( "EC:3.1.3.1") "glycerophosphatase activity") AnnotationAssertion(Annotation( "EC:3.1.3.1") "phosphomonoesterase activity") AnnotationAssertion( "EC:3.1.3.1") @@ -59944,8 +59869,9 @@ AnnotationAssertion(Annotation( "EC:2.3.1.21") AnnotationAssertion( "MetaCyc:CARNITINE-O-PALMITOYLTRANSFERASE-RXN") AnnotationAssertion( "RHEA:12661") -AnnotationAssertion(Annotation(rdfs:label "CPT1A,B transfers PALM to CAR") "Reactome:R-HSA-200406") -AnnotationAssertion(Annotation(rdfs:label "palmitoylcarnitine + CoASH => palmitoyl-CoA + carnitine") "Reactome:R-HSA-200410") +AnnotationAssertion(Annotation(rdfs:label "CPT1A transfers PALM to CAR") "Reactome:R-HSA-200406") +AnnotationAssertion(Annotation(rdfs:label "CPT2 converts palmitoyl carnitine to palmitoyl-CoA") "Reactome:R-HSA-200410") +AnnotationAssertion(Annotation(rdfs:label "CPT1B transfers PALM to CAR") "Reactome:R-HSA-9911362") AnnotationAssertion(Annotation( "EC:2.3.1.21") "CPT") AnnotationAssertion(Annotation( "EC:2.3.1.21") "CPT I (outer membrane carnitine palmitoyl transferase)") AnnotationAssertion(Annotation( "EC:2.3.1.21") "CPT-A") @@ -59973,8 +59899,7 @@ AnnotationAssertion( "KEGG_REACTION:R01082") AnnotationAssertion( "MetaCyc:FUMHYDR-RXN") AnnotationAssertion( "RHEA:12460") -AnnotationAssertion(Annotation(rdfs:label "(S)-Malate <=> Fumarate + H2O") "Reactome:R-HSA-451033") -AnnotationAssertion(Annotation(rdfs:label "Fumarate + H2O <=> (S)-Malate") "Reactome:R-HSA-70982") +AnnotationAssertion(Annotation(rdfs:label "FH tetramer hydrates fumarate to L-malate") "Reactome:R-HSA-70982") AnnotationAssertion(Annotation( "EC:4.2.1.2") "(S)-malate hydro-lyase (fumarate-forming)") AnnotationAssertion(Annotation( "EC:4.2.1.2") "(S)-malate hydro-lyase activity") AnnotationAssertion(Annotation( "EC:4.2.1.2") "L-malate hydro-lyase activity") @@ -60020,12 +59945,11 @@ SubClassOf( "PMID:12527308") "Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22621"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28526"^^xsd:anyURI) AnnotationAssertion( "GO:0103025") AnnotationAssertion(Annotation( "EC:3.2.1.1") "glycogenase activity") AnnotationAssertion( "EC:3.2.1.1") AnnotationAssertion( "MetaCyc:ALPHA-AMYL-RXN") -AnnotationAssertion( "MetaCyc:RXN-1823") -AnnotationAssertion( "MetaCyc:RXN-1825") AnnotationAssertion(Annotation(rdfs:label "Digestion of linear starch (amylose) by extracellular amylase") "Reactome:R-HSA-188979") AnnotationAssertion(Annotation(rdfs:label "Digestion of branched starch (amylopectin) by extracellular amylase") "Reactome:R-HSA-191114") AnnotationAssertion( "alpha-amylase activity (releasing maltohexaose)") @@ -60040,9 +59964,9 @@ SubClassOf( (beta-galactosidase activity) AnnotationAssertion(Annotation( "EC:3.2.1.23") "Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28526"^^xsd:anyURI) AnnotationAssertion( "EC:3.2.1.23") AnnotationAssertion( "MetaCyc:3.2.1.23-RXN") -AnnotationAssertion( "MetaCyc:BGALACT-PWY") AnnotationAssertion(Annotation(rdfs:label "Beta-galactosidases hydrolyse mobilized GM1 to mobilized GM2") "Reactome:R-HSA-1605624") AnnotationAssertion(Annotation(rdfs:label "GLB1 hydrolyzes SapB/C:LacCer") "Reactome:R-HSA-1606312") AnnotationAssertion(Annotation(rdfs:label "GLB1 hydrolyses a glycosaminoglycan") "Reactome:R-HSA-1630306") @@ -60062,76 +59986,6 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "beta-galactosidase activity") SubClassOf( ) -# Class: (phosphoglycerate kinase activity) - -AnnotationAssertion(Annotation( "EC:2.7.2.3") Annotation( "RHEA:14801") "Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H+.") -AnnotationAssertion( "EC:2.7.2.3") -AnnotationAssertion( "KEGG_REACTION:R01512") -AnnotationAssertion( "MetaCyc:PHOSGLYPHOS-RXN") -AnnotationAssertion( "RHEA:14801") -AnnotationAssertion(Annotation(rdfs:label "PGK complexes (PGK1,2) phosphorylate 3PG to form 1,3BPG") "Reactome:R-HSA-70486") -AnnotationAssertion(Annotation(rdfs:label "1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ATP") "Reactome:R-HSA-71850") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "3-PGK") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "3-phosphoglycerate kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "3-phosphoglycerate phosphokinase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "3-phosphoglyceric acid kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "3-phosphoglyceric acid phosphokinase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "3-phosphoglyceric kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "ATP-3-phospho-D-glycerate-1-phosphotransferase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "ATP:3-phospho-D-glycerate 1-phosphotransferase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "ATP:D-3-phosphoglycerate 1-phosphotransferase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "PGK") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "glycerate 3-phosphate kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "glycerophosphate kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "phosphoglyceric acid kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "phosphoglyceric kinase activity") -AnnotationAssertion(Annotation( "EC:2.7.2.3") "phosphoglycerokinase activity") -AnnotationAssertion( "GO:0004618") -AnnotationAssertion(rdfs:label "phosphoglycerate kinase activity") -SubClassOf( ) -SubClassOf( ) - -# Class: (phosphoglycerate mutase activity) - -AnnotationAssertion(Annotation( "RHEA:15901") "Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24905"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25780"^^xsd:anyURI) -AnnotationAssertion( "RHEA:15901") -AnnotationAssertion(Annotation(rdfs:label "PGAM dimers (PGAM1,2) isomerise 2PG to 3PG") "Reactome:R-HSA-71445") -AnnotationAssertion(Annotation(rdfs:label "3-Phospho-D-glycerate <=> 2-Phospho-D-glycerate") "Reactome:R-HSA-71654") -AnnotationAssertion( "PGM") -AnnotationAssertion( "D-phosphoglycerate 2,3-phosphomutase activity") -AnnotationAssertion( "PGA mutase activity") -AnnotationAssertion( "PGAM activity") -AnnotationAssertion( "phosphoglycerate phosphomutase activity") -AnnotationAssertion( "phosphoglyceromutase activity") -AnnotationAssertion( "GO:0004619") -AnnotationAssertion(rdfs:label "phosphoglycerate mutase activity") -SubClassOf( ) - -# Class: (phosphopyruvate hydratase activity) - -AnnotationAssertion(Annotation( "EC:4.2.1.11") Annotation( "ISBN:0198506732") "Catalysis of the reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O.") -AnnotationAssertion( "EC:4.2.1.11") -AnnotationAssertion( "MetaCyc:2PGADEHYDRAT-RXN") -AnnotationAssertion( "RHEA:10164") -AnnotationAssertion(Annotation(rdfs:label "Enolase dimers (ENO1,2,3) convert PEP to 2PG") "Reactome:R-HSA-70494") -AnnotationAssertion(Annotation(rdfs:label "2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O") "Reactome:R-HSA-71660") -AnnotationAssertion( "2-phospho-D-glycerate-hydrolase activity") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "nervous-system specific enolase") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "14-3-2-protein") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "2-phospho-D-glycerate hydro-lyase (phosphoenolpyruvate-forming)") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "2-phospho-D-glycerate hydro-lyase activity") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "2-phosphoglycerate dehydratase activity") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "2-phosphoglycerate enolase activity") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "2-phosphoglyceric dehydratase activity") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "enolase activity") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "gamma-enolase activity") -AnnotationAssertion(Annotation( "EC:4.2.1.11") "phosphoenolpyruvate hydratase activity") -AnnotationAssertion( "GO:0004634") -AnnotationAssertion(rdfs:label "phosphopyruvate hydratase activity") -SubClassOf( ) - # Class: (propionyl-CoA carboxylase activity) AnnotationAssertion(Annotation( "EC:6.4.1.3") "Catalysis of the reaction: ATP + propanoyl-CoA + HCO3- = ADP + phosphate + (S)-methylmalonyl-CoA.") @@ -60153,7 +60007,7 @@ AnnotationAssertion( "KEGG_REACTION:R00344") AnnotationAssertion( "MetaCyc:PYRUVATE-CARBOXYLASE-RXN") AnnotationAssertion( "RHEA:20844") -AnnotationAssertion(Annotation(rdfs:label "PC catalyzes the carboxylation of PYR to form OA") "Reactome:R-HSA-70501") +AnnotationAssertion(Annotation(rdfs:label "PC carboxylates PYR to OA") "Reactome:R-HSA-70501") AnnotationAssertion(Annotation( "EC:6.4.1.1") "pyruvate:carbon-dioxide ligase (ADP-forming)") AnnotationAssertion(Annotation( "EC:6.4.1.1") "pyruvic carboxylase activity") AnnotationAssertion( "GO:0004736") @@ -60184,6 +60038,7 @@ AnnotationAssertion( "Reactome:R-HSA-114552") AnnotationAssertion(Annotation(rdfs:label "Thrombin-activated PARs activate Gq") "Reactome:R-HSA-114558") AnnotationAssertion(Annotation(rdfs:label "The high affinity receptor complex binds to G-protein") "Reactome:R-HSA-167408") +AnnotationAssertion(Annotation(rdfs:label "GLP1R:GLP1 activates G(s)") "Reactome:R-HSA-381706") AnnotationAssertion( "Wikipedia:GPCR") AnnotationAssertion( "G protein coupled receptor activity") AnnotationAssertion( "G protein linked receptor activity") @@ -60519,23 +60374,12 @@ AnnotationAssertion(rdfs:label "mito SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (mitochondrial inner membrane) - -AnnotationAssertion(Annotation( "GOC:ai") "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.") -AnnotationAssertion( "NIF_Subcellular:sao1371347282") -AnnotationAssertion( "Wikipedia:Inner_mitochondrial_membrane") -AnnotationAssertion( "inner mitochondrial membrane") -AnnotationAssertion( "inner mitochondrion membrane") -AnnotationAssertion( "mitochondrion inner membrane") -AnnotationAssertion( "GO:0005743") -AnnotationAssertion(rdfs:label "mitochondrial inner membrane") -SubClassOf( ) -SubClassOf( ) - -# Class: (mitochondrial respirasome) +# Class: (obsolete mitochondrial respirasome) -AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:ecd") Annotation( "ISBN:0198547684") "The protein complexes that form the mitochondrial electron transport system (the respiratory chain), associated with the inner mitochondrial membrane. The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.") +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:ecd") Annotation( "ISBN:0198547684") "OBSOLETE. The protein complexes that form the mitochondrial electron transport system (the respiratory chain), associated with the inner mitochondrial membrane. The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/12846"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27253"^^xsd:anyURI) +AnnotationAssertion( "GO:0098803") AnnotationAssertion( "2012-02-23T05:13:54Z") AnnotationAssertion( "GO:0097249") AnnotationAssertion( "mitochondrial electron transport chain") @@ -60543,21 +60387,21 @@ AnnotationAssertion( "mitochondrial respiratory chain supercomplex") AnnotationAssertion( "mitochondrial respiratory supercomplex") AnnotationAssertion( "GO:0005746") -AnnotationAssertion(rdfs:label "mitochondrial respirasome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) +AnnotationAssertion(rdfs:comment "The reason for obsoletion is that this term unnecssarily specified a cellular compartment.") +AnnotationAssertion(rdfs:label "obsolete mitochondrial respirasome") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -# Class: (mitochondrial proton-transporting ATP synthase complex) +# Class: (obsolete mitochondrial proton-transporting ATP synthase complex) -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:mtg_sensu") "A proton-transporting ATP synthase complex found in the mitochondrial membrane.") +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:mtg_sensu") "OBSOLETE. A proton-transporting ATP synthase complex found in the mitochondrial membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27253"^^xsd:anyURI) +AnnotationAssertion( "GO:0045259") AnnotationAssertion( "GO:0016470") AnnotationAssertion( "mitochondrial respiratory chain complex V") AnnotationAssertion( "GO:0005753") -AnnotationAssertion(rdfs:label "mitochondrial proton-transporting ATP synthase complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) +AnnotationAssertion(rdfs:comment "The reason for obsoletion is that this term unnecssarily specified a cellular compartment.") +AnnotationAssertion(rdfs:label "obsolete mitochondrial proton-transporting ATP synthase complex") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Class: (mitochondrial matrix) @@ -60854,9 +60698,8 @@ SubClassOf( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27107"^^xsd:anyURI) -AnnotationAssertion( "MetaCyc:GLYCOGENSYNTH-PWY") -AnnotationAssertion( "MetaCyc:PWY-5067") -AnnotationAssertion( "MetaCyc:PWY-7900") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28527"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28968"^^xsd:anyURI) AnnotationAssertion( "glycogen anabolism") AnnotationAssertion( "glycogen biosynthesis") AnnotationAssertion( "glycogen formation") @@ -60884,9 +60727,7 @@ SubClassOf( ObjectSomeValuesFrom( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27107"^^xsd:anyURI) -AnnotationAssertion( "MetaCyc:GLYCOCAT-PWY") -AnnotationAssertion( "MetaCyc:PWY-5941") -AnnotationAssertion( "MetaCyc:PWY-7662") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28527"^^xsd:anyURI) AnnotationAssertion( "glycogen breakdown") AnnotationAssertion( "glycogen catabolism") AnnotationAssertion( "glycogen degradation") @@ -60954,7 +60795,6 @@ AnnotationAssertion( "aminoglycan metabolic process") SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (aminoglycan biosynthetic process) @@ -60968,7 +60808,6 @@ AnnotationAssertion(rdfs:label "amin SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (glycosaminoglycan biosynthetic process) @@ -60982,16 +60821,17 @@ AnnotationAssertion(rdfs:label "glyc SubClassOf( ) SubClassOf( ) -# Class: (cellular aldehyde metabolic process) +# Class: (aldehyde metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "aldehyde metabolism") AnnotationAssertion( "alkanal metabolic process") AnnotationAssertion( "alkanal metabolism") AnnotationAssertion( "GO:0006081") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular aldehyde metabolic process") -SubClassOf( ) +AnnotationAssertion(rdfs:label "aldehyde metabolic process") +SubClassOf( ) # Class: (organic acid metabolic process) @@ -61000,7 +60840,6 @@ AnnotationAssertion( "GO:0006082") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic acid metabolic process") -SubClassOf( ) SubClassOf( ) # Class: (lactate metabolic process) @@ -61016,19 +60855,6 @@ AnnotationAssertion(rdfs:label "lact SubClassOf( ) SubClassOf( ) -# Class: (pyruvate metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.") -AnnotationAssertion( "GO:0006087") -AnnotationAssertion( "MetaCyc:P41-PWY") -AnnotationAssertion( "Wikipedia:Pyruvic_acid") -AnnotationAssertion( "pyruvate metabolism") -AnnotationAssertion( "pyruvate dehydrogenase bypass") -AnnotationAssertion( "GO:0006090") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "pyruvate metabolic process") -SubClassOf( ) - # Class: (generation of precursor metabolites and energy) AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.") @@ -61050,12 +60876,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "generation of precursor metabolites and energy") -SubClassOf( ) +SubClassOf( ) # Class: (gluconeogenesis) AnnotationAssertion(Annotation( "MetaCyc:GLUCONEO-PWY") "The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.") -AnnotationAssertion( "MetaCyc:GLUCONEO-PWY") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28953"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Gluconeogenesis") AnnotationAssertion( "glucose biosynthesis") AnnotationAssertion( "glucose biosynthetic process") @@ -61064,32 +60890,6 @@ AnnotationAssertion(rdfs:label "gluc SubClassOf( ) SubClassOf( ) -# Class: (glycolytic process) - -AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dph") Annotation( "ISBN:0201090910") Annotation( "ISBN:0716720094") Annotation( "ISBN:0879010479") Annotation( "Wikipedia:Glycolysis") "The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21176"^^xsd:anyURI) -AnnotationAssertion( "GO:0019641") -AnnotationAssertion( "GO:0019642") -AnnotationAssertion( "MetaCyc:GLYCOLYSIS-VARIANTS") -AnnotationAssertion( "Embden-Meyerhof pathway") -AnnotationAssertion( "Embden-Meyerhof-Parnas pathway") -AnnotationAssertion( "anaerobic glycolysis") -AnnotationAssertion(Annotation( "GOC:dph") "glycolysis") -AnnotationAssertion( "modified Embden-Meyerhof pathway") -AnnotationAssertion( "GO:0006096") -AnnotationAssertion(rdfs:label "glycolytic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of carbohydrate metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.") @@ -61100,20 +60900,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of glycolytic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of glycolysis.") -AnnotationAssertion( "GO:0090525") -AnnotationAssertion( "regulation of glycolysis involved in cellular glucose homeostasis") -AnnotationAssertion( "GO:0006110") -AnnotationAssertion(rdfs:label "regulation of glycolytic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of gluconeogenesis) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.") @@ -61153,41 +60939,6 @@ AnnotationAssertion( "nucleobase-containing compound metabolic process") SubClassOf( ) -# Class: (regulation of nucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleotides.") -AnnotationAssertion( "regulation of nucleotide metabolism") -AnnotationAssertion( "GO:0006140") -AnnotationAssertion(rdfs:label "regulation of nucleotide metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (purine nucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.") -AnnotationAssertion( "purine nucleotide metabolism") -AnnotationAssertion( "purine metabolic process") -AnnotationAssertion( "purine metabolism") -AnnotationAssertion( "GO:0006163") -AnnotationAssertion(rdfs:label "purine nucleotide metabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (purine nucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.") -AnnotationAssertion( "purine nucleotide breakdown") -AnnotationAssertion( "purine nucleotide catabolism") -AnnotationAssertion( "purine nucleotide degradation") -AnnotationAssertion( "GO:0006195") -AnnotationAssertion(rdfs:label "purine nucleotide catabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - # 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.") @@ -61273,9 +61024,26 @@ AnnotationAssertion( "translation") SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translational initiation) + +AnnotationAssertion(Annotation( "ISBN:019879276X") "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.") +AnnotationAssertion( "GO:0006440") +AnnotationAssertion( "GO:0006454") +AnnotationAssertion( "biopolymerisation") +AnnotationAssertion( "biopolymerization") +AnnotationAssertion( "protein synthesis initiation") +AnnotationAssertion( "translation initiation") +AnnotationAssertion( "GO:0006413") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "translational initiation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (translational elongation) @@ -61290,6 +61058,19 @@ AnnotationAssertion(rdfs:label "tran SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (translational termination) + +AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "ISBN:019879276X") "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).") +AnnotationAssertion( "GO:0006443") +AnnotationAssertion( "GO:0006456") +AnnotationAssertion( "protein synthesis termination") +AnnotationAssertion( "translation termination") +AnnotationAssertion( "translational complex disassembly") +AnnotationAssertion( "GO:0006415") +AnnotationAssertion(rdfs:label "translational termination") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of translation) AnnotationAssertion(Annotation( "GOC:isa_complete") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.") @@ -61306,6 +61087,15 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of translational initiation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of translational initiation.") +AnnotationAssertion( "GO:0006446") +AnnotationAssertion(rdfs:label "regulation of translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of translational elongation) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate, extent or accuracy of translational elongation.") @@ -61315,6 +61105,16 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of translational termination) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of translational termination.") +AnnotationAssertion( "GO:0006449") +AnnotationAssertion(rdfs:label "regulation of translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (protein glycosylation) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:pr") "A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.") @@ -61346,7 +61146,7 @@ SubClassOf( (protein O-linked glycosylation) -AnnotationAssertion(Annotation( "GOC:pr") Annotation( "ISBN:0879695595") Annotation( "RESID:AA0153") Annotation( "RESID:AA0154") Annotation( "RESID:AA0155") Annotation( "RESID:AA0157") Annotation( "RESID:AA0212") "A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or via the phenol group of peptidyl-tyrosine, forming an O-glycan.") +AnnotationAssertion(Annotation( "GOC:pr") Annotation( "ISBN:0879695595") Annotation( "PMID:33775405") "A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or via the phenol group of peptidyl-tyrosine, forming an O-glycan.") AnnotationAssertion( "RESID:AA0153") AnnotationAssertion( "RESID:AA0154") AnnotationAssertion( "RESID:AA0155") @@ -61392,15 +61192,14 @@ AnnotationAssertion( "amino acid metabolic process") SubClassOf( ) -# Class: (regulation of cellular amino acid metabolic process) +# Class: (regulation of amino acid metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "regulation of amino acid metabolism") AnnotationAssertion( "GO:0006521") -AnnotationAssertion(rdfs:label "regulation of cellular amino acid metabolic process") +AnnotationAssertion(rdfs:label "regulation of amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -61416,22 +61215,22 @@ AnnotationAssertion(rdfs:label "meth SubClassOf( ) SubClassOf( ) -# Class: (cellular modified amino acid metabolic process) +# Class: (modified amino acid metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "amino acid derivative metabolic process") AnnotationAssertion( "cellular amino acid derivative metabolic process") AnnotationAssertion( "cellular amino acid derivative metabolism") +AnnotationAssertion(Annotation( "GOC:mah") "cellular modified amino acid metabolic process") AnnotationAssertion(Annotation( "GOC:mah") "cellular modified amino acid metabolism") -AnnotationAssertion(Annotation( "GOC:mah") "modified amino acid metabolic process") AnnotationAssertion(Annotation( "GOC:mah") "modified amino acid metabolism") AnnotationAssertion( "GO:0006575") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular modified amino acid metabolic process") -SubClassOf( ) -SubClassOf( ) +AnnotationAssertion(rdfs:label "modified amino acid metabolic process") +SubClassOf( ) # Class: (melanin metabolic process) @@ -61489,20 +61288,23 @@ SubClassOf( (fatty acid metabolic process) AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Fatty_acid_metabolism") AnnotationAssertion( "fatty acid metabolism") AnnotationAssertion( "GO:0006631") AnnotationAssertion(rdfs:label "fatty acid metabolic process") +SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (membrane lipid metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving membrane lipids, any lipid found in or associated with a biological membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "membrane lipid metabolism") AnnotationAssertion( "GO:0006643") AnnotationAssertion(rdfs:label "membrane lipid metabolic process") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glycolipid metabolic process) @@ -61520,7 +61322,6 @@ AnnotationAssertion( "GO:0006665") AnnotationAssertion(rdfs:label "sphingolipid metabolic process") SubClassOf( ) -SubClassOf( ) # Class: (ceramide metabolic process) @@ -61623,6 +61424,7 @@ SubClassOf( (isoprenoid metabolic process) AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways involving isoprenoid compounds, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "GO:0016096") AnnotationAssertion( "isoprenoid metabolism") AnnotationAssertion( "polyisoprenoid metabolic process") @@ -61631,7 +61433,7 @@ AnnotationAssertion( "polyterpene metabolism") AnnotationAssertion( "GO:0006720") AnnotationAssertion(rdfs:label "isoprenoid metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (terpenoid metabolic process) @@ -61641,16 +61443,6 @@ AnnotationAssertion( "terpenoid metabolic process") SubClassOf( ) -# Class: (nucleoside phosphate metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving any phosphorylated nucleoside.") -AnnotationAssertion( "nucleoside phosphate metabolism") -AnnotationAssertion( "GO:0006753") -AnnotationAssertion(rdfs:label "nucleoside phosphate metabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - # Class: (vitamin metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.") @@ -61705,7 +61497,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sulfur compound metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (phosphorus metabolic process) @@ -61714,7 +61506,7 @@ AnnotationAssertion( "GO:0006793") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phosphorus metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (phosphate-containing compound metabolic process) @@ -61985,6 +61777,8 @@ AnnotationAssertion( "GO:0006915") AnnotationAssertion(rdfs:label "apoptotic process") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cellular component disassembly involved in execution phase of apoptosis) @@ -62060,9 +61854,19 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (syncytium formation) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.") +AnnotationAssertion( "GO:0006949") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "syncytium formation") +SubClassOf( ) +SubClassOf( ) + # Class: (response to stress) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26810"^^xsd:anyURI) AnnotationAssertion( "response to abiotic stress") AnnotationAssertion( "response to biotic stress") AnnotationAssertion( "GO:0006950") @@ -62072,7 +61876,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "response to stress") SubClassOf( ) @@ -62495,6 +62298,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "G protein-coupled receptor signaling pathway") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cell-cell signaling) @@ -63107,17 +62911,14 @@ AnnotationAssertion(rdfs:label "biol # Class: (metabolic process) -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198547684") "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.") +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28932"^^xsd:anyURI) AnnotationAssertion( "2012-10-17T15:46:40Z") AnnotationAssertion( "GO:0044236") AnnotationAssertion( "GO:0044710") AnnotationAssertion( "Wikipedia:Metabolism") AnnotationAssertion( "metabolism") -AnnotationAssertion( "metabolic process resulting in cell growth") -AnnotationAssertion( "metabolism resulting in cell growth") -AnnotationAssertion( "multicellular organism metabolic process") -AnnotationAssertion( "single-organism metabolic process") AnnotationAssertion( "GO:0008152") AnnotationAssertion( ) AnnotationAssertion( ) @@ -63128,7 +62929,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.") AnnotationAssertion(rdfs:label "metabolic process") -SubClassOf( ) +SubClassOf( ) DisjointClasses( ) DisjointClasses( ) @@ -63168,7 +62969,6 @@ AnnotationAssertion( "GO:0008212") AnnotationAssertion(rdfs:label "mineralocorticoid metabolic process") SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (regulation of blood pressure) @@ -63308,10 +63108,10 @@ SubClassOf( (sulfite oxidase activity) -AnnotationAssertion(Annotation( "EC:1.8.3.1") Annotation( "RHEA:24600") "Catalysis of the reaction: H2O + O2 + sulfite = H2O2 + H+ + sulfate.") +AnnotationAssertion(Annotation( "RHEA:24600") "Catalysis of the reaction: H2O + O2 + sulfite = H2O2 + H+ + sulfate.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28526"^^xsd:anyURI) AnnotationAssertion( "EC:1.8.3.1") AnnotationAssertion( "KEGG_REACTION:R00533") -AnnotationAssertion( "MetaCyc:PWY-5326") AnnotationAssertion( "MetaCyc:SULFITE-OXIDASE-RXN") AnnotationAssertion( "RHEA:24600") AnnotationAssertion(Annotation(rdfs:label "Sulfite is oxidized to sulfate") "Reactome:R-HSA-1614544") @@ -63324,7 +63124,7 @@ SubClassOf( (transaminase activity) -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.") +AnnotationAssertion(Annotation( "EC:2.6.1.-") "Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.") AnnotationAssertion( "EC:2.6.1.-") AnnotationAssertion(Annotation(rdfs:label "Transamination of MOB to methionine") "Reactome:R-HSA-1237102") AnnotationAssertion( "aminotransferase activity") @@ -63394,16 +63194,18 @@ SubClassOf( (catabolic process) -AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.") +AnnotationAssertion(Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism breaks down substances. This includes the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28921"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28932"^^xsd:anyURI) AnnotationAssertion( "2012-10-17T15:52:35Z") AnnotationAssertion( "GO:0044243") AnnotationAssertion( "GO:0044712") AnnotationAssertion( "Wikipedia:Catabolism") -AnnotationAssertion( "breakdown") +AnnotationAssertion( "breakdown of chemical") +AnnotationAssertion( "breakdown of molecule") +AnnotationAssertion( "breakdown of substance") AnnotationAssertion( "catabolism") AnnotationAssertion( "degradation") -AnnotationAssertion( "multicellular organismal catabolic process") -AnnotationAssertion( "single-organism catabolic process") AnnotationAssertion( "GO:0009056") AnnotationAssertion( ) AnnotationAssertion( ) @@ -63433,7 +63235,8 @@ SubClassOf( (biosynthetic process) -AnnotationAssertion(Annotation( "GOC:curators") Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.") +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28932"^^xsd:anyURI) AnnotationAssertion( "2012-10-17T15:52:18Z") AnnotationAssertion( "GO:0044274") AnnotationAssertion( "GO:0044711") @@ -63469,8 +63272,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "macromolecule biosynthetic process") +SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (aspartate family amino acid metabolic process) @@ -63503,159 +63306,6 @@ AnnotationAssertion(rdfs:label "glyc SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) - -# Class: (nucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:ma") "The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).") -AnnotationAssertion( "nucleotide metabolism") -AnnotationAssertion( "GO:0009117") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "nucleotide metabolic process") -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( "GO:0009132") -AnnotationAssertion(rdfs:label "nucleoside diphosphate metabolic process") -SubClassOf( ) - -# 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( "GO:0009134") -AnnotationAssertion(rdfs:label "nucleoside diphosphate catabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (purine nucleoside diphosphate metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar.") -AnnotationAssertion( "purine nucleoside diphosphate metabolism") -AnnotationAssertion( "GO:0009135") -AnnotationAssertion(rdfs:label "purine nucleoside diphosphate metabolic process") -SubClassOf( ) - -# Class: (purine nucleoside diphosphate catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar.") -AnnotationAssertion( "purine nucleoside diphosphate breakdown") -AnnotationAssertion( "purine nucleoside diphosphate catabolism") -AnnotationAssertion( "purine nucleoside diphosphate degradation") -AnnotationAssertion( "GO:0009137") -AnnotationAssertion(rdfs:label "purine nucleoside diphosphate catabolic process") -SubClassOf( ) -SubClassOf( ) - -# 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( "GO:0009141") -AnnotationAssertion(rdfs:label "nucleoside triphosphate metabolic process") -SubClassOf( ) - -# Class: (purine nucleoside triphosphate metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar.") -AnnotationAssertion( "purine nucleoside triphosphate metabolism") -AnnotationAssertion( "GO:0009144") -AnnotationAssertion(rdfs:label "purine nucleoside triphosphate metabolic process") -SubClassOf( ) - -# Class: (purine ribonucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.") -AnnotationAssertion( "purine ribonucleotide metabolism") -AnnotationAssertion( "GO:0009150") -AnnotationAssertion(rdfs:label "purine ribonucleotide metabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (purine ribonucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.") -AnnotationAssertion( "purine ribonucleotide breakdown") -AnnotationAssertion( "purine ribonucleotide catabolism") -AnnotationAssertion( "purine ribonucleotide degradation") -AnnotationAssertion( "GO:0009154") -AnnotationAssertion(rdfs:label "purine ribonucleotide catabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - -# Class: (nucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).") -AnnotationAssertion( "nucleotide breakdown") -AnnotationAssertion( "nucleotide catabolism") -AnnotationAssertion( "nucleotide degradation") -AnnotationAssertion( "GO:0009166") -AnnotationAssertion(rdfs:label "nucleotide catabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (purine ribonucleoside diphosphate metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar.") -AnnotationAssertion( "purine ribonucleoside diphosphate metabolism") -AnnotationAssertion( "GO:0009179") -AnnotationAssertion(rdfs:label "purine ribonucleoside diphosphate metabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (purine ribonucleoside diphosphate catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar.") -AnnotationAssertion( "purine ribonucleoside diphosphate breakdown") -AnnotationAssertion( "purine ribonucleoside diphosphate catabolism") -AnnotationAssertion( "purine ribonucleoside diphosphate degradation") -AnnotationAssertion( "GO:0009181") -AnnotationAssertion(rdfs:label "purine ribonucleoside diphosphate catabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - -# Class: (ribonucleoside diphosphate metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar.") -AnnotationAssertion( "ribonucleoside diphosphate metabolism") -AnnotationAssertion( "GO:0009185") -AnnotationAssertion(rdfs:label "ribonucleoside diphosphate metabolic process") -SubClassOf( ) - -# Class: (ribonucleoside diphosphate catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar.") -AnnotationAssertion( "ribonucleoside diphosphate breakdown") -AnnotationAssertion( "ribonucleoside diphosphate catabolism") -AnnotationAssertion( "ribonucleoside diphosphate degradation") -AnnotationAssertion( "GO:0009191") -AnnotationAssertion(rdfs:label "ribonucleoside diphosphate catabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (ribonucleoside triphosphate metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar.") -AnnotationAssertion( "ribonucleoside triphosphate metabolism") -AnnotationAssertion( "GO:0009199") -AnnotationAssertion(rdfs:label "ribonucleoside triphosphate metabolic process") -SubClassOf( ) - -# Class: (purine ribonucleoside triphosphate metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar.") -AnnotationAssertion( "purine ribonucleoside triphosphate metabolism") -AnnotationAssertion( "GO:0009205") -AnnotationAssertion(rdfs:label "purine ribonucleoside triphosphate metabolic process") -SubClassOf( ) -SubClassOf( ) # Class: (cobalamin metabolic process) @@ -63692,28 +63342,6 @@ AnnotationAssertion(rdfs:label "gluc SubClassOf( ) SubClassOf( ) -# Class: (ribonucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.") -AnnotationAssertion( "GO:0009121") -AnnotationAssertion( "ribonucleotide metabolism") -AnnotationAssertion( "GO:0009259") -AnnotationAssertion(rdfs:label "ribonucleotide metabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (ribonucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.") -AnnotationAssertion( "ribonucleotide breakdown") -AnnotationAssertion( "ribonucleotide catabolism") -AnnotationAssertion( "ribonucleotide degradation") -AnnotationAssertion( "GO:0009261") -AnnotationAssertion(rdfs:label "ribonucleotide catabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - # Class: (nucleoid) AnnotationAssertion(Annotation( "GOC:bm") Annotation( "GOC:ma") Annotation( "ISBN:3540076689") "The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.") @@ -63736,19 +63364,6 @@ SubClassOf( ) SubClassOf( ) -# Class: (amine metabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.") -AnnotationAssertion( "2009-07-15T11:55:44Z") -AnnotationAssertion( "GO:0044106") -AnnotationAssertion( "amine metabolism") -AnnotationAssertion( "cellular amine metabolic process") -AnnotationAssertion( "GO:0009308") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "amine metabolic process") -SubClassOf( ) - # Class: (response to radiation) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "Wikipedia:Electromagnetic_radiation") "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 electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.") @@ -63770,7 +63385,7 @@ SubClassOf( (methylglyoxal metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving methylglyoxal, CH3-CO-CHO, the aldehyde of pyruvic acid.") -AnnotationAssertion( "MetaCyc:METHGLYUT-PWY") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28388"^^xsd:anyURI) AnnotationAssertion( "methylglyoxal metabolism") AnnotationAssertion( "methylglyoxal bypass") AnnotationAssertion( "methylglyoxal pathway") @@ -64054,7 +63669,7 @@ AnnotationAssertion( "negative regulation of metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of metabolic process) @@ -64075,7 +63690,7 @@ AnnotationAssertion( "positive regulation of metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of catabolic process) @@ -64309,7 +63924,7 @@ AnnotationAssertion(Annotation( "regulation of receptor activity") AnnotationAssertion( "regulation of signalling receptor activity") AnnotationAssertion( "GO:0010469") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of signaling receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -64352,7 +63967,7 @@ AnnotationAssertion(Annotation( "GO:0010556") AnnotationAssertion(rdfs:label "regulation of macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -64362,9 +63977,9 @@ AnnotationAssertion(Annotation( "GO:0010557") AnnotationAssertion(rdfs:label "positive regulation of macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of macromolecule biosynthetic process) @@ -64373,9 +63988,9 @@ AnnotationAssertion(Annotation( "GO:0010558") AnnotationAssertion(rdfs:label "negative regulation of macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of glycoprotein biosynthetic process) @@ -64416,7 +64031,7 @@ AnnotationAssertion(Annotation( "GO:0010562") AnnotationAssertion(rdfs:label "positive regulation of phosphorus metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -64426,7 +64041,7 @@ AnnotationAssertion(Annotation( "GO:0010563") AnnotationAssertion(rdfs:label "negative regulation of phosphorus metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -64439,14 +64054,14 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of cellular ketone metabolic process) +# Class: (regulation of ketone metabolic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "GO:0010565") -AnnotationAssertion(rdfs:label "regulation of cellular ketone metabolic process") +AnnotationAssertion(rdfs:label "regulation of ketone metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of ketone catabolic process) @@ -64455,8 +64070,9 @@ AnnotationAssertion(Annotation( "GO:0010567") AnnotationAssertion(rdfs:label "regulation of ketone catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of platelet activation) @@ -64591,7 +64207,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of alkaline phosphatase activity, the catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.") AnnotationAssertion( "GO:0010692") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of alkaline phosphatase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -64601,7 +64217,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate or extent of alkaline phosphatase activity, the catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.") AnnotationAssertion( "GO:0010693") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of alkaline phosphatase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -64612,7 +64228,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of alkaline phosphatase activity, the catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.") AnnotationAssertion( "GO:0010694") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of alkaline phosphatase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -64676,33 +64292,36 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of glucose transmembrane transport) +# Class: (regulation of D-glucose transmembrane transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "regulation of glucose transmembrane transport") AnnotationAssertion( "regulation of glucose transport") AnnotationAssertion( "GO:0010827") -AnnotationAssertion(rdfs:label "regulation of glucose transmembrane transport") +AnnotationAssertion(rdfs:label "regulation of D-glucose transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (positive regulation of glucose transmembrane transport) +# Class: (positive regulation of D-glucose transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "positive regulation of glucose transmembrane transport") AnnotationAssertion( "positive regulation of glucose transport") AnnotationAssertion( "GO:0010828") -AnnotationAssertion(rdfs:label "positive regulation of glucose transmembrane transport") +AnnotationAssertion(rdfs:label "positive regulation of D-glucose transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of glucose transmembrane transport) +# Class: (negative regulation of D-glucose transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "negative regulation of glucose transmembrane transport") AnnotationAssertion( "negative regulation of glucose transport") AnnotationAssertion( "GO:0010829") -AnnotationAssertion(rdfs:label "negative regulation of glucose transmembrane transport") +AnnotationAssertion(rdfs:label "negative regulation of D-glucose transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -64774,7 +64393,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.") AnnotationAssertion( "GO:0010911") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of isomerase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -64784,7 +64403,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.") AnnotationAssertion( "GO:0010912") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of isomerase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -64795,7 +64414,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing phosphate.") AnnotationAssertion( "GO:0010921") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of phosphatase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -64806,7 +64425,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.") AnnotationAssertion( "GO:0010922") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of phosphatase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -64818,7 +64437,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.") AnnotationAssertion( "GO:0010923") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of phosphatase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -64922,6 +64541,7 @@ AnnotationAssertion( "Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.") AnnotationAssertion(rdfs:label "programmed cell death") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endomembrane system) @@ -65406,7 +65026,7 @@ SubClassOf( "GOC:ai") "Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26780"^^xsd:anyURI) -AnnotationAssertion( "RHEA:28695") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27521"^^xsd:anyURI) AnnotationAssertion(Annotation(rdfs:label "BESTs transport cytosolic HCO3- to extracellular region") "Reactome:R-HSA-2752067") AnnotationAssertion( "hydrogencarbonate transmembrane transporter activity") AnnotationAssertion( "GO:0015106") @@ -65720,7 +65340,6 @@ AnnotationAssertion( "GO:0016053") AnnotationAssertion(rdfs:label "organic acid biosynthetic process") SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (immunoglobulin mediated immune response) @@ -65792,42 +65411,13 @@ AnnotationAssertion( "inclusion body") SubClassOf( ) -# Class: (kinase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") -AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") -AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") -AnnotationAssertion( "phosphokinase activity") -AnnotationAssertion( "GO:0016301") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") -AnnotationAssertion(rdfs:label "kinase activity") -SubClassOf( ) - -# Class: (phosphorylation) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "Wikipedia:Phosphorylation") -AnnotationAssertion( "GO:0016310") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphorylation") -SubClassOf( ) - # Class: (dephosphorylation) AnnotationAssertion(Annotation( "ISBN:0198506732") "The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Dephosphorylation") AnnotationAssertion( "GO:0016311") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dephosphorylation") SubClassOf( ) @@ -65859,7 +65449,6 @@ SubClassOf( "GOC:ai") "Catalysis of the transfer of a palmitoyl (CH3-[CH2]14-CO-) group to an acceptor molecule.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27365"^^xsd:anyURI) -AnnotationAssertion(Annotation(rdfs:label "palmitoylation of eNOS") "Reactome:R-HSA-203567") AnnotationAssertion(Annotation(rdfs:label "ZDHHC2 transfers PALM from PALM-CoA to CKAP4") "Reactome:R-HSA-5686304") AnnotationAssertion( "GO:0016409") AnnotationAssertion(rdfs:comment "Note that this term should not be confused with 'palmitoleoyltransferase activity ; GO:1990698'.") @@ -65918,19 +65507,6 @@ AnnotationAssertion(rdfs:label "soma SubClassOf( ) SubClassOf( ) -# Class: (proton-transporting two-sector ATPase complex) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0716743663") Annotation( "PMID:16691483") "A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane. The complex comprises a membrane sector (F0, V0, or A0) that carries out proton transport and a cytoplasmic compartment sector (F1, V1, or A1) that catalyzes ATP synthesis or hydrolysis. Two major types have been characterized: V-type ATPases couple ATP hydrolysis to the transport of protons across a concentration gradient, whereas F-type ATPases, also known as ATP synthases, normally run in the reverse direction to utilize energy from a proton concentration or electrochemical gradient to synthesize ATP. A third type, A-type ATPases have been found in archaea, and are closely related to eukaryotic V-type ATPases but are reversible.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15936"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28017"^^xsd:anyURI) -AnnotationAssertion( "hydrogen-transporting two-sector ATPase complex") -AnnotationAssertion( "vacuolar hydrogen-transporting ATPase") -AnnotationAssertion( "GO:0016469") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "proton-transporting two-sector ATPase complex") -SubClassOf( ) - # Class: (cell migration) AnnotationAssertion(Annotation( "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.") @@ -65956,19 +65532,21 @@ SubClassOf( (oxidoreductase activity) -AnnotationAssertion(Annotation( "GOC:go_curators") "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.") +AnnotationAssertion(Annotation( "EC:1.-.-.-") "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.") AnnotationAssertion( "EC:1.-.-.-") AnnotationAssertion(Annotation(rdfs:label "SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases") "Reactome:R-HSA-1614362") AnnotationAssertion(Annotation(rdfs:label "Monoiodinated tyrosine can be deiodinated") "Reactome:R-HSA-209921") AnnotationAssertion(Annotation(rdfs:label "Diiodinated tyrosine can be deiodinated") "Reactome:R-HSA-209960") -AnnotationAssertion(Annotation(rdfs:label "MMACHC dealkylates RCbl") "Reactome:R-HSA-3095889") +AnnotationAssertion(Annotation(rdfs:label "PGH2 is reduced to PGF2a by FAM213B") "Reactome:R-HSA-2161612") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is oxidised to 5S-HpETE by ALOX5") "Reactome:R-HSA-265296") +AnnotationAssertion(Annotation(rdfs:label "5S-HpETE is dehydrated to LTA4 by ALOX5") "Reactome:R-HSA-266051") AnnotationAssertion(Annotation(rdfs:label "FAR1 reduces PalmCoA to HXOL") "Reactome:R-HSA-390425") AnnotationAssertion(Annotation(rdfs:label "FAR2 reduces PalmCoA to HXOL") "Reactome:R-HSA-390438") AnnotationAssertion(Annotation(rdfs:label "Dopachrome is transformed to DHICA by DCT") "Reactome:R-HSA-5662660") AnnotationAssertion(Annotation(rdfs:label "TYRP1 oxidises DHICA to IQCA") "Reactome:R-HSA-8878581") AnnotationAssertion(Annotation(rdfs:label "MARC1,MARC2 reduce N-hydroxylated compounds") "Reactome:R-HSA-8936442") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6") "Reactome:R-HSA-9020249") -AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reducatse reduces 7(S)-Hp-17(S)-HDHA to RvD5") "Reactome:R-HSA-9020260") +AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 7(S)-Hp-17(S)-HDHA to RvD5") "Reactome:R-HSA-9020260") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6") "Reactome:R-HSA-9024624") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5") "Reactome:R-HSA-9024630") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1") "Reactome:R-HSA-9025007") @@ -65976,6 +65554,7 @@ AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 7,17-di AnnotationAssertion(Annotation(rdfs:label "Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA") "Reactome:R-HSA-9026917") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA") "Reactome:R-HSA-9027033") AnnotationAssertion(Annotation(rdfs:label "Unknown sepiapterin synthase transforms PTHP to sepiapterin") "Reactome:R-HSA-9693722") +AnnotationAssertion(Annotation(rdfs:label "Cob(I)alamin bound to MMACHC is oxidized to cob(II)alamin") "Reactome:R-HSA-9759549") AnnotationAssertion( "redox activity") AnnotationAssertion( "oxidoreductase activity, acting on other substrates") AnnotationAssertion( "GO:0016491") @@ -66019,20 +65598,14 @@ SubClassOf( "EC:1.1.1.-") "Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.") AnnotationAssertion( "EC:1.1.1.-") +AnnotationAssertion(Annotation(rdfs:label "5-HEDH dehydrogenates 7-HDPAn-3 to 7-oxo-DPAn-3") "Reactome:R-HSA-9027625") +AnnotationAssertion(Annotation(rdfs:label "5-HEDH dehydrogenates 7-HDHA to 7-oxo-DHA") "Reactome:R-HSA-9027631") +AnnotationAssertion(Annotation(rdfs:label "5-HEDH dehydrogenates 5-HEPE to 5-oxo-EPA") "Reactome:R-HSA-9027632") AnnotationAssertion(Annotation(rdfs:label "RDH11 reduces RBP2:atRAL to RBP2:atROL") "Reactome:R-HSA-975629") AnnotationAssertion( "GO:0016616") AnnotationAssertion(rdfs:label "oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor") SubClassOf( ) -# Class: (oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor) - -AnnotationAssertion(Annotation( "GOC:jl") "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.") -AnnotationAssertion( "EC:1.2.1.-") -AnnotationAssertion(Annotation(rdfs:label "MscR reduces nitrosomycothiol to ammonia") "Reactome:R-HSA-1222583") -AnnotationAssertion( "GO:0016620") -AnnotationAssertion(rdfs:label "oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor") -SubClassOf( ) - # Class: (oxidoreductase activity, acting on a sulfur group of donors) AnnotationAssertion(Annotation( "GOC:ai") "Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.") @@ -66055,7 +65628,7 @@ SubClassOf( (transferase activity) -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") +AnnotationAssertion(Annotation( "EC:2.-.-.-") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") AnnotationAssertion( "EC:2.-.-.-") AnnotationAssertion(Annotation(rdfs:label "PE is converted to PS by PTDSS2") "Reactome:R-HSA-1483089") AnnotationAssertion(Annotation(rdfs:label "PC is converted to PS by PTDSS1") "Reactome:R-HSA-1483186") @@ -66084,7 +65657,6 @@ AnnotationAssertion( "Reactome:R-HSA-159431") AnnotationAssertion(Annotation(rdfs:label "Choloyl CoA reacts with glycine or taurine to form glycocholate or taurocholate") "Reactome:R-HSA-192312") AnnotationAssertion(Annotation(rdfs:label "Chenodeoxycholoyl CoA reacts with glycine or taurine to form glycochenodeoxycholate or taurochenodeoxycholate") "Reactome:R-HSA-193491") -AnnotationAssertion(Annotation(rdfs:label "LIPT1 transfers lipoyl group from lipoyl-GCSH to DHs") "Reactome:R-HSA-6792572") AnnotationAssertion(Annotation(rdfs:label "HRASLS transfer acyl group from PC to PE to form NAPE") "Reactome:R-HSA-8858298") AnnotationAssertion( "transferase activity, transferring acyl groups") AnnotationAssertion( "GO:0016746") @@ -66098,6 +65670,8 @@ SubClassOf( "EC:2.3.1.-") "Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20486"^^xsd:anyURI) AnnotationAssertion( "EC:2.3.1.-") +AnnotationAssertion(Annotation(rdfs:label "DBT transfers BCAA to CoA") "Reactome:R-HSA-9859163") +AnnotationAssertion(Annotation(rdfs:label "DBT loss-of-function mutants don't synthesize BCAA-CoA") "Reactome:R-HSA-9865115") AnnotationAssertion( "transferase activity, transferring acyl groups other than amino-acyl groups") AnnotationAssertion(Annotation( "EC:2.3.1.-") "transferase activity, transferring groups other than amino-acyl groups") AnnotationAssertion( "GO:0016747") @@ -66113,24 +65687,6 @@ AnnotationAssertion( "transferase activity, transferring nitrogenous groups") SubClassOf( ) -# Class: (transferase activity, transferring phosphorus-containing groups) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") -AnnotationAssertion( "EC:2.7.-.-") -AnnotationAssertion( "GO:0016772") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.") -AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups") -SubClassOf( ) - -# Class: (phosphotransferase activity, carboxyl group as acceptor) - -AnnotationAssertion(Annotation( "GOC:jl") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a carboxyl group (acceptor).") -AnnotationAssertion( "EC:2.7.2.-") -AnnotationAssertion( "GO:0016774") -AnnotationAssertion(rdfs:label "phosphotransferase activity, carboxyl group as acceptor") -SubClassOf( ) - # Class: (hydrolase activity) AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.") @@ -66210,7 +65766,7 @@ SubClassOf( (lyase activity) -AnnotationAssertion(Annotation( "ISBN:0198547684") "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.") +AnnotationAssertion(Annotation( "EC:4.-.-.-") "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.") AnnotationAssertion( "EC:4.-.-.-") AnnotationAssertion(Annotation(rdfs:label "PXLP-K278-PHYKPL tetramer hydrolyses 5PHL") "Reactome:R-HSA-5696408") AnnotationAssertion(Annotation(rdfs:label "TYW1:FMN:4Fe-4S transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) at nucleotide 37 of tRNA(Phe)") "Reactome:R-HSA-6782895") @@ -66239,6 +65795,7 @@ SubClassOf( "EC:4.2.1.-") "Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.") AnnotationAssertion( "EC:4.2.1.-") +AnnotationAssertion(Annotation(rdfs:label "PGE2 is dehydrated to PGA2") "Reactome:R-HSA-2161659") AnnotationAssertion(Annotation(rdfs:label "SDS dimers:PXLP dehydrate L-Thr to 2AA") "Reactome:R-HSA-9014627") AnnotationAssertion( "GO:0016836") AnnotationAssertion(rdfs:label "hydro-lyase activity") @@ -66248,6 +65805,8 @@ SubClassOf( "ISBN:0198506732") "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.") AnnotationAssertion( "EC:5.-.-.-") +AnnotationAssertion(Annotation(rdfs:label "PGA2 is isomerised to PGC2") "Reactome:R-HSA-2161666") +AnnotationAssertion(Annotation(rdfs:label "PGC2 is isomerised to PGB2") "Reactome:R-HSA-2161735") AnnotationAssertion(Annotation(rdfs:label "TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal") "Reactome:R-HSA-6787623") AnnotationAssertion( "other isomerase activity") AnnotationAssertion( "GO:0016853") @@ -66272,22 +65831,9 @@ AnnotationAssertion( "intramolecular transferase activity") SubClassOf( ) -# Class: (intramolecular phosphotransferase activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Catalysis of the transfer of a phosphate group from one position to another within a single molecule.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26155"^^xsd:anyURI) -AnnotationAssertion( "GO:0016777") -AnnotationAssertion( "EC:5.4.2.-") -AnnotationAssertion( "intramolecular transferase activity, phosphotransferases") -AnnotationAssertion( "phosphomutase activity") -AnnotationAssertion( "phosphotransferase activity, with regeneration of donors, apparently catalyzing intramolecular transfers") -AnnotationAssertion( "GO:0016868") -AnnotationAssertion(rdfs:label "intramolecular phosphotransferase activity") -SubClassOf( ) - # Class: (ligase activity) -AnnotationAssertion(Annotation( "GOC:mah") "Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.") +AnnotationAssertion(Annotation( "EC:6.-.-.-") "Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19380"^^xsd:anyURI) AnnotationAssertion( "EC:6.-.-.-") AnnotationAssertion(Annotation( "GOC:jh2") "synthetase activity") @@ -66312,15 +65858,6 @@ AnnotationAssertion( "ligase activity, forming carbon-carbon bonds") SubClassOf( ) -# Class: (oxidoreductase activity, acting on the aldehyde or oxo group of donors) - -AnnotationAssertion(Annotation( "GOC:ai") "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.") -AnnotationAssertion( "EC:1.2.-.-") -AnnotationAssertion( "oxidoreductase activity, acting on the aldehyde or oxo group of donors, other acceptors") -AnnotationAssertion( "GO:0016903") -AnnotationAssertion(rdfs:label "oxidoreductase activity, acting on the aldehyde or oxo group of donors") -SubClassOf( ) - # Class: (stem cell division) AnnotationAssertion(Annotation( "GOC:jid") Annotation( "ISBN:0582227089") "The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.") @@ -66431,6 +65968,7 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of steroid metabolic process) @@ -66485,7 +66023,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (transmission of nerve impulse) @@ -66552,27 +66090,6 @@ AnnotationAssertion(rdfs:label "hexo SubClassOf( ) SubClassOf( ) -# Class: (pyridine nucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways involving a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.") -AnnotationAssertion( "pyridine nucleotide metabolism") -AnnotationAssertion( "GO:0019362") -AnnotationAssertion(rdfs:label "pyridine nucleotide metabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (pyridine nucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:pde") Annotation( "GOC:vw") "The chemical reactions and pathways resulting in the breakdown of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.") -AnnotationAssertion( "pyridine nucleotide breakdown") -AnnotationAssertion( "pyridine nucleotide catabolism") -AnnotationAssertion( "pyridine nucleotide degradation") -AnnotationAssertion( "GO:0019364") -AnnotationAssertion(rdfs:label "pyridine nucleotide catabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - # Class: (protein metabolic process) AnnotationAssertion(Annotation( "GOC:ma") "The chemical reactions and pathways involving a protein. Includes protein modification.") @@ -66600,27 +66117,6 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "protein metabolic process") SubClassOf( ) SubClassOf( ) -SubClassOf( ) - -# Class: (organophosphate metabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26992"^^xsd:anyURI) -AnnotationAssertion( "organophosphate metabolism") -AnnotationAssertion( "GO:0019637") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organophosphate metabolic process") -SubClassOf( ) - -# Class: (ribose phosphate metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar.") -AnnotationAssertion( "ribose phosphate metabolism") -AnnotationAssertion( "GO:0019693") -AnnotationAssertion(rdfs:label "ribose phosphate metabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) # Class: (B cell mediated immunity) @@ -66664,7 +66160,6 @@ AnnotationAssertion( "regulation of isoprenoid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (secondary metabolic process) @@ -66734,15 +66229,6 @@ SubClassOf( ) SubClassOf( ) -# Class: (organelle inner membrane) - -AnnotationAssertion(Annotation( "GOC:mah") "The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites.") -AnnotationAssertion( "GO:0019866") -AnnotationAssertion(rdfs:comment "See also the cellular component term 'outer membrane ; GO:0019867'.") -AnnotationAssertion(rdfs:label "organelle inner membrane") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (antigen processing and presentation) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GO_REF:0000022") Annotation( "ISBN:0781735149") Annotation( "PMID:15771591") Annotation( "PMID:15928678") "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.") @@ -66841,6 +66327,14 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "cell cycle phase") SubClassOf( ) +# Class: (membrane docking) + +AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "PMID:27875684") "The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere.") +AnnotationAssertion( "GO:0022406") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "membrane docking") +SubClassOf( ) + # Class: (regulation of cell-cell adhesion) AnnotationAssertion(Annotation( "GOC:isa_complete") "Any process that modulates the frequency, rate or extent of attachment of a cell to another cell.") @@ -66976,6 +66470,28 @@ AnnotationAssertion(rdfs:label "cell SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (ribonucleoprotein complex biogenesis) + +AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:mah") "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.") +AnnotationAssertion(Annotation( "GOC:mah") "RNA-protein complex biogenesis") +AnnotationAssertion(Annotation( "GOC:mah") "ribonucleoprotein complex biogenesis and assembly") +AnnotationAssertion( "GO:0022613") +AnnotationAssertion(rdfs:label "ribonucleoprotein complex biogenesis") +SubClassOf( ) + +# Class: (protein-RNA complex assembly) + +AnnotationAssertion(Annotation( "GOC:jl") "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.") +AnnotationAssertion( "RNA-protein complex assembly") +AnnotationAssertion( "RNP complex assembly") +AnnotationAssertion( "ribonucleoprotein complex assembly") +AnnotationAssertion( "GO:0022618") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "protein-RNA complex assembly") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:jid") Annotation( "GOC:mtg_transport") Annotation( "ISBN:0815340729") "Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.") @@ -67007,7 +66523,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:dph") Annotation( "GOC:mtg_cardio") Annotation( "GOC:mtg_transport") "Any process that modulates the frequency, rate or extent of transmembrane transporter activity.") AnnotationAssertion( "GO:0022898") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of transmembrane transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -67838,56 +67354,6 @@ AnnotationAssertion( "cytoskeleton-dependent intracellular transport") SubClassOf( ) -# Class: (regulation of nucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides.") -AnnotationAssertion( "regulation of nucleotide breakdown") -AnnotationAssertion( "regulation of nucleotide catabolism") -AnnotationAssertion( "regulation of nucleotide degradation") -AnnotationAssertion( "GO:0030811") -AnnotationAssertion(rdfs:label "regulation of nucleotide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of nucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides.") -AnnotationAssertion( "down regulation of nucleotide catabolic process") -AnnotationAssertion( "down-regulation of nucleotide catabolic process") -AnnotationAssertion( "downregulation of nucleotide catabolic process") -AnnotationAssertion( "negative regulation of nucleotide breakdown") -AnnotationAssertion( "negative regulation of nucleotide catabolism") -AnnotationAssertion( "negative regulation of nucleotide degradation") -AnnotationAssertion( "inhibition of nucleotide catabolic process") -AnnotationAssertion( "GO:0030812") -AnnotationAssertion(rdfs:label "negative regulation of nucleotide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of nucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides.") -AnnotationAssertion( "positive regulation of nucleotide breakdown") -AnnotationAssertion( "positive regulation of nucleotide catabolism") -AnnotationAssertion( "positive regulation of nucleotide degradation") -AnnotationAssertion( "up regulation of nucleotide catabolic process") -AnnotationAssertion( "up-regulation of nucleotide catabolic process") -AnnotationAssertion( "upregulation of nucleotide catabolic process") -AnnotationAssertion( "activation of nucleotide catabolic process") -AnnotationAssertion( "stimulation of nucleotide catabolic process") -AnnotationAssertion( "GO:0030813") -AnnotationAssertion(rdfs:label "positive regulation of nucleotide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (granulocyte differentiation) AnnotationAssertion(Annotation( "GOC:ecd") Annotation( "http://life.nthu.edu.tw/~g864204/dict-search1.htm") "The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.") @@ -68182,179 +67648,37 @@ AnnotationAssertion( "pseudopodium organization") SubClassOf( ) -# Class: (regulation of cellular metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "regulation of cellular metabolism") -AnnotationAssertion( "GO:0031323") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "regulation of cellular metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of cellular metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "down regulation of cellular metabolic process") -AnnotationAssertion( "down-regulation of cellular metabolic process") -AnnotationAssertion( "downregulation of cellular metabolic process") -AnnotationAssertion( "negative regulation of cellular metabolism") -AnnotationAssertion( "inhibition of cellular metabolic process") -AnnotationAssertion( "GO:0031324") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "negative regulation of cellular metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of cellular metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "positive regulation of cellular metabolism") -AnnotationAssertion( "up regulation of cellular metabolic process") -AnnotationAssertion( "up-regulation of cellular metabolic process") -AnnotationAssertion( "upregulation of cellular metabolic process") -AnnotationAssertion( "activation of cellular metabolic process") -AnnotationAssertion( "stimulation of cellular metabolic process") -AnnotationAssertion( "GO:0031325") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "positive regulation of cellular metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (regulation of cellular biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "regulation of cellular anabolism") -AnnotationAssertion( "regulation of cellular biosynthesis") -AnnotationAssertion( "regulation of cellular formation") -AnnotationAssertion( "regulation of cellular synthesis") -AnnotationAssertion( "GO:0031326") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "regulation of cellular biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of cellular biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "down regulation of cellular biosynthetic process") -AnnotationAssertion( "down-regulation of cellular biosynthetic process") -AnnotationAssertion( "downregulation of cellular biosynthetic process") -AnnotationAssertion( "negative regulation of cellular anabolism") -AnnotationAssertion( "negative regulation of cellular biosynthesis") -AnnotationAssertion( "negative regulation of cellular formation") -AnnotationAssertion( "negative regulation of cellular synthesis") -AnnotationAssertion( "inhibition of cellular biosynthetic process") -AnnotationAssertion( "GO:0031327") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "negative regulation of cellular biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of cellular biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "positive regulation of cellular anabolism") -AnnotationAssertion( "positive regulation of cellular biosynthesis") -AnnotationAssertion( "positive regulation of cellular formation") -AnnotationAssertion( "positive regulation of cellular synthesis") -AnnotationAssertion( "up regulation of cellular biosynthetic process") -AnnotationAssertion( "up-regulation of cellular biosynthetic process") -AnnotationAssertion( "upregulation of cellular biosynthetic process") -AnnotationAssertion( "activation of cellular biosynthetic process") -AnnotationAssertion( "stimulation of cellular biosynthetic process") -AnnotationAssertion( "GO:0031328") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "positive regulation of cellular biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (regulation of cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "regulation of cellular breakdown") -AnnotationAssertion( "regulation of cellular catabolism") -AnnotationAssertion( "regulation of cellular degradation") -AnnotationAssertion( "GO:0031329") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "regulation of cellular catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "down regulation of cellular catabolic process") -AnnotationAssertion( "down-regulation of cellular catabolic process") -AnnotationAssertion( "downregulation of cellular catabolic process") -AnnotationAssertion( "negative regulation of cellular breakdown") -AnnotationAssertion( "negative regulation of cellular catabolism") -AnnotationAssertion( "negative regulation of cellular degradation") -AnnotationAssertion( "inhibition of cellular catabolic process") -AnnotationAssertion( "GO:0031330") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "negative regulation of cellular catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "positive regulation of cellular breakdown") -AnnotationAssertion( "positive regulation of cellular catabolism") -AnnotationAssertion( "positive regulation of cellular degradation") -AnnotationAssertion( "up regulation of cellular catabolic process") -AnnotationAssertion( "up-regulation of cellular catabolic process") -AnnotationAssertion( "upregulation of cellular catabolic process") -AnnotationAssertion( "activation of cellular catabolic process") -AnnotationAssertion( "stimulation of cellular catabolic process") -AnnotationAssertion( "GO:0031331") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "positive regulation of cellular catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of protein-containing complex assembly) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.") +AnnotationAssertion( "down regulation of protein complex assembly") +AnnotationAssertion( "down-regulation of protein complex assembly") +AnnotationAssertion( "downregulation of protein complex assembly") +AnnotationAssertion( "inhibition of protein complex assembly") +AnnotationAssertion( "negative regulation of protein complex assembly") +AnnotationAssertion( "GO:0031333") +AnnotationAssertion(rdfs:label "negative regulation of protein-containing complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of protein-containing complex assembly) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of protein complex assembly.") +AnnotationAssertion( "up regulation of protein complex assembly") +AnnotationAssertion( "up-regulation of protein complex assembly") +AnnotationAssertion( "upregulation of protein complex assembly") +AnnotationAssertion( "activation of protein complex assembly") +AnnotationAssertion( "stimulation of protein complex assembly") +AnnotationAssertion( "positive regulation of protein complex assembly") +AnnotationAssertion( "GO:0031334") +AnnotationAssertion(rdfs:label "positive regulation of protein-containing complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of sulfur amino acid metabolic process) @@ -68579,6 +67903,7 @@ AnnotationAssertion( "downregulation of protein modification") AnnotationAssertion( "inhibition of protein modification") AnnotationAssertion( "GO:0031400") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of protein modification process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -68594,6 +67919,7 @@ AnnotationAssertion( "activation of protein modification") AnnotationAssertion( "stimulation of protein modification") AnnotationAssertion( "GO:0031401") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of protein modification process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -68785,7 +68111,6 @@ AnnotationAssertion( "regulation of glucocorticoid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -68800,7 +68125,6 @@ AnnotationAssertion( "GO:0031944") AnnotationAssertion(rdfs:label "negative regulation of glucocorticoid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -68818,7 +68142,6 @@ AnnotationAssertion( "GO:0031945") AnnotationAssertion(rdfs:label "positive regulation of glucocorticoid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -68989,6 +68312,33 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (negative regulation of translational initiation in response to stress) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents or reduces the rate of translation initiation as a result of a stimulus indicating the organism is under stress.") +AnnotationAssertion( "down regulation of translation initiation in response to stress") +AnnotationAssertion( "down-regulation of translation initiation in response to stress") +AnnotationAssertion( "downregulation of translation initiation in response to stress") +AnnotationAssertion( "inhibition of translation initiation in response to stress") +AnnotationAssertion( "GO:0032057") +AnnotationAssertion(rdfs:label "negative regulation of translational initiation in response to stress") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translational initiation in response to stress) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of translation initiation as a result of a stimulus indicating the organism is under stress.") +AnnotationAssertion( "up regulation of translation initiation in response to stress") +AnnotationAssertion( "up-regulation of translation initiation in response to stress") +AnnotationAssertion( "upregulation of translation initiation in response to stress") +AnnotationAssertion( "activation of translation initiation in response to stress") +AnnotationAssertion( "stimulation of translation initiation in response to stress") +AnnotationAssertion( "GO:0032058") +AnnotationAssertion(rdfs:label "positive regulation of translational initiation in response to stress") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (bleb assembly) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:12083798") Annotation( "PMID:16624291") Annotation( "Wikipedia:Bleb_(cell_biology)") "The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.") @@ -69325,7 +68675,7 @@ AnnotationAssertion( "GO:0032353") AnnotationAssertion(rdfs:label "negative regulation of hormone biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -69416,7 +68766,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mah") "Any process that modulates the activity of a transporter.") AnnotationAssertion( "GO:0032409") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -69430,7 +68780,7 @@ AnnotationAssertion( "downregulation of transporter activity") AnnotationAssertion( "inhibition of transporter activity") AnnotationAssertion( "GO:0032410") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -69447,7 +68797,7 @@ AnnotationAssertion( "activation of transporter activity") AnnotationAssertion( "stimulation of transporter activity") AnnotationAssertion( "GO:0032411") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of transporter activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -69902,6 +69252,22 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing complex disassembly) + +AnnotationAssertion(Annotation( "GOC:mah") "The disaggregation of a protein-containing macromolecular complex into its constituent components.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22580"^^xsd:anyURI) +AnnotationAssertion( "GO:0034623") +AnnotationAssertion( "GO:0043241") +AnnotationAssertion( "GO:0043624") +AnnotationAssertion( "protein complex disassembly") +AnnotationAssertion( "cellular macromolecule complex disassembly") +AnnotationAssertion( "cellular protein complex disassembly") +AnnotationAssertion( "macromolecule complex disassembly") +AnnotationAssertion( "GO:0032984") +AnnotationAssertion(rdfs:label "protein-containing complex disassembly") +SubClassOf( ) +SubClassOf( ) + # Class: (cellular anatomical entity morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:tb") "The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system.") @@ -69934,16 +69300,6 @@ AnnotationAssertion(rdfs:comment "A AnnotationAssertion(rdfs:label "protein-containing complex") SubClassOf( ) -# Class: (protein-DNA complex) - -AnnotationAssertion(Annotation( "GOC:mah") "A macromolecular complex containing both protein and DNA molecules.") -AnnotationAssertion(Annotation( "GOC:mah") "DNA-protein complex") -AnnotationAssertion( "GO:0032993") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here.") -AnnotationAssertion(rdfs:label "protein-DNA complex") -SubClassOf( ) - # Class: (protein-lipid complex) AnnotationAssertion(Annotation( "GOC:mah") "A macromolecular complex containing separate protein and lipid molecules. Separate in this context means not covalently bound to each other.") @@ -69981,7 +69337,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tetrapyrrole metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (macromolecule localization) @@ -70055,47 +69411,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of purine nucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides.") -AnnotationAssertion( "regulation of purine nucleotide breakdown") -AnnotationAssertion( "regulation of purine nucleotide catabolism") -AnnotationAssertion( "regulation of purine nucleotide degradation") -AnnotationAssertion( "GO:0033121") -AnnotationAssertion(rdfs:label "regulation of purine nucleotide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of purine nucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides.") -AnnotationAssertion( "negative regulation of purine nucleotide breakdown") -AnnotationAssertion( "negative regulation of purine nucleotide catabolism") -AnnotationAssertion( "negative regulation of purine nucleotide degradation") -AnnotationAssertion( "GO:0033122") -AnnotationAssertion(rdfs:label "negative regulation of purine nucleotide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of purine nucleotide catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides.") -AnnotationAssertion( "positive regulation of purine nucleotide breakdown") -AnnotationAssertion( "positive regulation of purine nucleotide catabolism") -AnnotationAssertion( "positive regulation of purine nucleotide degradation") -AnnotationAssertion( "GO:0033123") -AnnotationAssertion(rdfs:label "positive regulation of purine nucleotide catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (V(D)J recombination) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781700221") Annotation( "ISBN:0781735149") "The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).") @@ -70132,41 +69447,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of amine metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines.") -AnnotationAssertion( "regulation of amine metabolism") -AnnotationAssertion( "regulation of cellular amine metabolic process") -AnnotationAssertion( "GO:0033238") -AnnotationAssertion(rdfs:label "regulation of amine metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of amine metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines.") -AnnotationAssertion( "negative regulation of amine metabolism") -AnnotationAssertion( "negative regulation of cellular amine metabolic process") -AnnotationAssertion( "GO:0033239") -AnnotationAssertion(rdfs:label "negative regulation of amine metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of amine metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines.") -AnnotationAssertion( "positive regulation of amine metabolism") -AnnotationAssertion( "positive regulation of cellular amine metabolic process") -AnnotationAssertion( "GO:0033240") -AnnotationAssertion(rdfs:label "positive regulation of amine metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (secretory granule organization) AnnotationAssertion(Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion.") @@ -70196,9 +69476,8 @@ SubClassOf( (cellular response to stress) 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 stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26810"^^xsd:anyURI) AnnotationAssertion( "GO:0033554") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "cellular response to stress") SubClassOf( ) SubClassOf( ) @@ -70206,8 +69485,7 @@ SubClassOf( (unsaturated fatty acid metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving an unsaturated fatty acid, any fatty acid containing one or more double bonds between carbon atoms.") -AnnotationAssertion( "MetaCyc:PWY-762") -AnnotationAssertion( "MetaCyc:PWY-782") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28388"^^xsd:anyURI) AnnotationAssertion( "unsaturated fatty acid metabolism") AnnotationAssertion( "GO:0033559") AnnotationAssertion(rdfs:label "unsaturated fatty acid metabolic process") @@ -70273,40 +69551,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of kinase activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces 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( "down regulation of kinase activity") -AnnotationAssertion( "down-regulation of kinase activity") -AnnotationAssertion( "downregulation of kinase activity") -AnnotationAssertion( "inhibition of kinase activity") -AnnotationAssertion( "kinase inhibitor") -AnnotationAssertion( "GO:0033673") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of kinase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of kinase activity) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases 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( "up regulation of kinase activity") -AnnotationAssertion( "up-regulation of kinase activity") -AnnotationAssertion( "upregulation of kinase activity") -AnnotationAssertion( "kinase activator") -AnnotationAssertion( "stimulation of kinase activity") -AnnotationAssertion( "GO:0033674") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of kinase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of luteinizing hormone secretion) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the regulated release of luteinizing hormone.") @@ -70456,6 +69700,17 @@ AnnotationAssertion(rdfs:label "mono SubClassOf( ) SubClassOf( ) +# Class: (negative regulation of syncytium formation by plasma membrane fusion) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that decreases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.") +AnnotationAssertion( "GO:0034242") +AnnotationAssertion(rdfs:label "negative regulation of syncytium formation by plasma membrane fusion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of amide metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides.") @@ -70518,34 +69773,6 @@ AnnotationAssertion(rdfs:label "toot SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (nucleobase-containing compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.") -AnnotationAssertion( "nucleobase, nucleoside, nucleotide and nucleic acid breakdown") -AnnotationAssertion( "nucleobase, nucleoside, nucleotide and nucleic acid catabolism") -AnnotationAssertion( "nucleobase, nucleoside, nucleotide and nucleic acid degradation") -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process") -AnnotationAssertion( "GO:0034655") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "nucleobase-containing compound catabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (monoatomic ion channel complex) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:071673706X") "A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective monoatomic ion transport down its electrochemical gradient.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20026"^^xsd:anyURI) -AnnotationAssertion( "GO:0034702") -AnnotationAssertion(rdfs:label "monoatomic ion channel complex") -SubClassOf( ) - -# Class: (cation channel complex) - -AnnotationAssertion(Annotation( "GOC:mah") "An ion channel complex through which cations pass.") -AnnotationAssertion( "GO:0034703") -AnnotationAssertion(rdfs:label "cation channel complex") -SubClassOf( ) - # Class: (regulation of transmembrane transport) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other.") @@ -70919,6 +70146,16 @@ SubClassOf( ) SubClassOf( ) +# Class: (glomerular endothelium fenestra) + +AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "MP:0011454") Annotation( "PMID:19129259") "A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes.") +AnnotationAssertion( "2011-12-12T10:53:24Z") +AnnotationAssertion(Annotation( "PMID:19129259") "GEnC fenestration") +AnnotationAssertion(Annotation( "PMID:19129259") "glomerular endothelial cell fenestration") +AnnotationAssertion( "GO:0036053") +AnnotationAssertion(rdfs:label "glomerular endothelium fenestra") +SubClassOf( ) + # Class: (fucosylation) AnnotationAssertion(Annotation( "GOC:sart") Annotation( "PMID:19948734") "The covalent attachment of a fucosyl group to an acceptor molecule.") @@ -71356,15 +70593,15 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (cellular ketone metabolic process) +# Class: (ketone metabolic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0787650153") "The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "ketone metabolism") AnnotationAssertion( "GO:0042180") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular ketone metabolic process") -SubClassOf( ) -SubClassOf( ) +AnnotationAssertion(rdfs:label "ketone metabolic process") +SubClassOf( ) # Class: (ketone catabolic process) @@ -71375,7 +70612,6 @@ AnnotationAssertion( "GO:0042182") AnnotationAssertion(rdfs:label "ketone catabolic process") SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (response to chemical) @@ -71444,50 +70680,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of phosphorylation) - -AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "GO:0042325") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "regulation of phosphorylation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of phosphorylation) - -AnnotationAssertion(Annotation( "GOC:jl") "Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "down regulation of phosphorylation") -AnnotationAssertion( "down-regulation of phosphorylation") -AnnotationAssertion( "downregulation of phosphorylation") -AnnotationAssertion( "inhibition of phosphorylation") -AnnotationAssertion( "GO:0042326") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "negative regulation of phosphorylation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of phosphorylation) - -AnnotationAssertion(Annotation( "GOC:jl") "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.") -AnnotationAssertion( "up regulation of phosphorylation") -AnnotationAssertion( "up-regulation of phosphorylation") -AnnotationAssertion( "upregulation of phosphorylation") -AnnotationAssertion( "activation of phosphorylation") -AnnotationAssertion( "stimulation of phosphorylation") -AnnotationAssertion( "GO:0042327") -AnnotationAssertion(rdfs:label "positive regulation of phosphorylation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (taxis) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0192801023") "The directed movement of a motile cell or organism in response to an external stimulus.") @@ -71578,7 +70770,7 @@ AnnotationAssertion( "indole derivative metabolism") AnnotationAssertion( "GO:0042430") AnnotationAssertion(rdfs:label "indole-containing compound metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (indole-containing compound biosynthetic process) @@ -71591,8 +70783,8 @@ AnnotationAssertion( "indole-containing compound synthesis") AnnotationAssertion( "GO:0042435") AnnotationAssertion(rdfs:label "indole-containing compound biosynthetic process") +SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (pigment metabolic process) @@ -72038,7 +71230,7 @@ AnnotationAssertion( "GO:0042762") AnnotationAssertion(rdfs:label "regulation of sulfur metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (amide transport) @@ -72243,7 +71435,7 @@ AnnotationAssertion( "up-regulation of metalloenzyme activity") AnnotationAssertion( "upregulation of metalloenzyme activity") AnnotationAssertion( "GO:0043085") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -72266,7 +71458,7 @@ AnnotationAssertion( "inhibition of metalloenzyme activity") AnnotationAssertion( "negative regulation of metalloenzyme activity") AnnotationAssertion( "GO:0043086") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -72364,30 +71556,39 @@ SubClassOf( (membrane-bounded organelle) AnnotationAssertion(Annotation( "GOC:go_curators") "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28153"^^xsd:anyURI) AnnotationAssertion( "NIF_Subcellular:sao414196390") AnnotationAssertion( "membrane-enclosed organelle") AnnotationAssertion( "GO:0043227") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "membrane-bounded organelle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (non-membrane-bounded organelle) +# Class: (membraneless organelle) AnnotationAssertion(Annotation( "GOC:go_curators") "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21881"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28153"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29106"^^xsd:anyURI) AnnotationAssertion( "NIF_Subcellular:sao1456184038") +AnnotationAssertion( "membrane-less organelle") +AnnotationAssertion( "non-membrane-bounded organelle") AnnotationAssertion( "non-membrane-enclosed organelle") AnnotationAssertion( "biological condensate") AnnotationAssertion( "GO:0043228") +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "non-membrane-bounded organelle") +AnnotationAssertion(rdfs:label "membraneless organelle") SubClassOf( ) # Class: (intracellular organelle) AnnotationAssertion(Annotation( "GOC:go_curators") "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28153"^^xsd:anyURI) AnnotationAssertion( "GO:0043229") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "intracellular organelle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -72415,13 +71616,15 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (intracellular non-membrane-bounded organelle) +# Class: (intracellular membraneless organelle) AnnotationAssertion(Annotation( "GOC:go_curators") "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29106"^^xsd:anyURI) +AnnotationAssertion( "intracellular non-membrane-bounded organelle") AnnotationAssertion( "intracellular non-membrane-enclosed organelle") AnnotationAssertion( "GO:0043232") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "intracellular non-membrane-bounded organelle") +AnnotationAssertion(rdfs:label "intracellular membraneless organelle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -72444,6 +71647,58 @@ AnnotationAssertion( "receptor complex") SubClassOf( ) +# Class: (negative regulation of protein-containing complex disassembly) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.") +AnnotationAssertion( "down regulation of protein complex disassembly") +AnnotationAssertion( "down-regulation of protein complex disassembly") +AnnotationAssertion( "downregulation of protein complex disassembly") +AnnotationAssertion( "inhibition of protein complex disassembly") +AnnotationAssertion( "negative regulation of protein complex disassembly") +AnnotationAssertion( "GO:0043242") +AnnotationAssertion(rdfs:label "negative regulation of protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of protein-containing complex disassembly) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.") +AnnotationAssertion( "up regulation of protein complex disassembly") +AnnotationAssertion( "up-regulation of protein complex disassembly") +AnnotationAssertion( "upregulation of protein complex disassembly") +AnnotationAssertion( "activation of protein complex disassembly") +AnnotationAssertion( "stimulation of protein complex disassembly") +AnnotationAssertion( "positive regulation of protein complex disassembly") +AnnotationAssertion( "GO:0043243") +AnnotationAssertion(rdfs:label "positive regulation of protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of protein-containing complex disassembly) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.") +AnnotationAssertion( "regulation of protein complex disassembly") +AnnotationAssertion( "GO:0043244") +AnnotationAssertion(rdfs:label "regulation of protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of protein-containing complex assembly) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of protein complex assembly.") +AnnotationAssertion( "regulation of protein complex assembly") +AnnotationAssertion( "GO:0043254") +AnnotationAssertion(rdfs:label "regulation of protein-containing complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of carbohydrate biosynthetic process) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates.") @@ -72458,12 +71713,14 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (extracellular non-membrane-bounded organelle) +# Class: (extracellular membraneless organelle) AnnotationAssertion(Annotation( "GOC:jl") "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29106"^^xsd:anyURI) +AnnotationAssertion( "extracellular non-membrane-bounded organelle") AnnotationAssertion( "extracellular non-membrane-enclosed organelle") AnnotationAssertion( "GO:0043264") -AnnotationAssertion(rdfs:label "extracellular non-membrane-bounded organelle") +AnnotationAssertion(rdfs:label "extracellular membraneless organelle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -72617,7 +71874,7 @@ SubClassOf( "GOC:go_curators") "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "GO:0043412") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macromolecule modification") SubClassOf( ) @@ -72660,7 +71917,7 @@ AnnotationAssertion(Annotation( "GO:0043467") AnnotationAssertion(rdfs:label "regulation of generation of precursor metabolites and energy") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of carbohydrate catabolic process) @@ -72702,17 +71959,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (regulation of kinase activity) - -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( "GO:0043549") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of kinase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of translation in response to stress) AnnotationAssertion(Annotation( "GOC:jl") "Modulation of the frequency, rate or extent of translation as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).") @@ -72723,6 +71969,16 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of translational initiation in response to stress) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of translation initiation, as a result of a stimulus indicating the organism is under stress.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:hjd") Annotation( "GOC:tb") "regulation of translation initiation in response to stress") +AnnotationAssertion( "GO:0043558") +AnnotationAssertion(rdfs:label "regulation of translational initiation in response to stress") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (regulation of respiratory gaseous exchange) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment.") @@ -72761,20 +72017,6 @@ AnnotationAssertion(rdfs:label "amid SubClassOf( ) SubClassOf( ) -# Class: (glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity) - -AnnotationAssertion(Annotation( "EC:1.2.1.59") "Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H + H+.") -AnnotationAssertion( "EC:1.2.1.59") -AnnotationAssertion( "MetaCyc:GAPDHSYNEC-RXN") -AnnotationAssertion( "D-glyceraldehyde 3-phosphate:NAD(P)+ oxidoreductase (phosphorylating)") -AnnotationAssertion( "glyceraldehyde-3-phosphate dehydrogenase (NAD(P)) (phosphorylating)") -AnnotationAssertion( "triosephosphate dehydrogenase (NAD(P))") -AnnotationAssertion(Annotation( "EC:1.2.1.59") "NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase activity") -AnnotationAssertion(Annotation( "EC:1.2.1.59") "triosephosphate dehydrogenase (NAD(P)+)") -AnnotationAssertion( "GO:0043891") -AnnotationAssertion(rdfs:label "glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity") -SubClassOf( ) - # Class: (regulation of biological process involved in symbiotic interaction) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association.") @@ -72811,6 +72053,27 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing complex organization) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22580"^^xsd:anyURI) +AnnotationAssertion( "2010-09-08T10:01:42Z") +AnnotationAssertion( "GO:0034600") +AnnotationAssertion( "GO:0034621") +AnnotationAssertion( "GO:0071822") +AnnotationAssertion(Annotation( "GOC:mah") "protein complex subunit organisation") +AnnotationAssertion( "protein complex subunit organization") +AnnotationAssertion( "cellular macromolecular complex organization") +AnnotationAssertion( "cellular macromolecular complex subunit organisation") +AnnotationAssertion( "cellular macromolecular complex subunit organization") +AnnotationAssertion( "macromolecular complex organization") +AnnotationAssertion( "macromolecular complex subunit organisation") +AnnotationAssertion( "macromolecular complex subunit organization") +AnnotationAssertion( "protein-containing complex subunit organization") +AnnotationAssertion( "GO:0043933") +AnnotationAssertion(rdfs:label "protein-containing complex organization") +SubClassOf( ) + # Class: (glucan metabolic process) AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.") @@ -72870,9 +72133,11 @@ SubClassOf( ObjectSomeValuesFrom( (cellular component biogenesis) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mah") "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "GO:0071843") AnnotationAssertion( "cellular component biogenesis at cellular level") AnnotationAssertion( "GO:0044085") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component biogenesis") SubClassOf( ) @@ -72912,24 +72177,12 @@ SubClassOf( ObjectSomeValuesFrom( "GO:jl") "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.") AnnotationAssertion( "2009-04-21T04:11:06Z") AnnotationAssertion( "GO:0044093") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of molecular function") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (cellular metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways by which individual cells transform chemical substances.") -AnnotationAssertion( "cellular metabolism") -AnnotationAssertion(Annotation( "GOC:mah") "intermediary metabolism") -AnnotationAssertion( "GO:0044237") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") -AnnotationAssertion(rdfs:label "cellular metabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (primary metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.") @@ -72945,42 +72198,6 @@ AnnotationAssertion( "primary metabolic process") SubClassOf( ) -# Class: (cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "cellular breakdown") -AnnotationAssertion( "cellular catabolism") -AnnotationAssertion( "cellular degradation") -AnnotationAssertion( "GO:0044248") -AnnotationAssertion(rdfs:label "cellular catabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (cellular biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27052"^^xsd:anyURI) -AnnotationAssertion( "cellular anabolism") -AnnotationAssertion( "cellular biosynthesis") -AnnotationAssertion( "cellular formation") -AnnotationAssertion( "cellular synthesis") -AnnotationAssertion( "GO:0044249") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") -AnnotationAssertion(rdfs:label "cellular biosynthetic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (cellular lipid metabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways involving lipids, as carried out by individual cells.") -AnnotationAssertion( "cellular lipid metabolism") -AnnotationAssertion( "GO:0044255") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular lipid metabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (sulfur compound biosynthetic process) AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.") @@ -72993,7 +72210,7 @@ AnnotationAssertion( "GO:0044272") AnnotationAssertion(rdfs:label "sulfur compound biosynthetic process") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (small molecule metabolic process) @@ -73156,6 +72373,17 @@ DisjointClasses( ) DisjointClasses( ) +# Class: (plasma membrane fusion) + +AnnotationAssertion(Annotation( "GOC:elh") Annotation( "GOC:mtg_muscle") "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.") +AnnotationAssertion( "GO:0006947") +AnnotationAssertion( "cell fusion") +AnnotationAssertion( "cell-cell fusion") +AnnotationAssertion( "GO:0045026") +AnnotationAssertion(rdfs:label "plasma membrane fusion") +SubClassOf( ) +SubClassOf( ) + # Class: (T cell selection) AnnotationAssertion(Annotation( "ISBN:0781735149") Annotation( "PMID:12414722") "The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation.") @@ -73351,35 +72579,6 @@ AnnotationAssertion( "external encapsulating structure organization") SubClassOf( ) -# Class: (proton-transporting ATP synthase complex) - -AnnotationAssertion(Annotation( "ISBN:0198547684") Annotation( "ISBN:0716743663") "A proton-transporting two-sector ATPase complex that catalyzes the phosphorylation of ADP to ATP during oxidative phosphorylation. The complex comprises a membrane sector (F0) that carries out proton transport and a cytoplasmic compartment sector (F1) that catalyzes ATP synthesis by a rotational mechanism; the extramembrane sector (containing 3 a and 3 b subunits) is connected via the d-subunit to the membrane sector by several smaller subunits. Within this complex, the g and e subunits and the 9-12 c subunits rotate by consecutive 120 degree angles and perform parts of ATP synthesis. This movement is driven by the hydrogen ion electrochemical potential gradient.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28017"^^xsd:anyURI) -AnnotationAssertion( "GO:0045255") -AnnotationAssertion( "F1-F0 complex") -AnnotationAssertion( "hydrogen-translocating F-type ATPase complex") -AnnotationAssertion( "hydrogen-transporting ATP synthase complex") -AnnotationAssertion( "proton-transporting F-type ATPase complex") -AnnotationAssertion( "GO:0045259") -AnnotationAssertion(rdfs:label "proton-transporting ATP synthase complex") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - -# Class: (plasma membrane proton-transporting ATP synthase complex) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:mtg_sensu") Annotation( "ISBN:0198547684") "A proton-transporting ATP synthase complex found in the plasma membrane. Examples of this component are found in Bacterial species.") -AnnotationAssertion( "GO:0045256") -AnnotationAssertion( "hydrogen-translocating F-type ATPase complex") -AnnotationAssertion( "proton-transporting ATP synthase complex") -AnnotationAssertion( "hydrogen-transporting ATP synthase") -AnnotationAssertion( "plasma membrane hydrogen-translocating F-type ATPase complex") -AnnotationAssertion( "GO:0045260") -AnnotationAssertion(rdfs:label "plasma membrane proton-transporting ATP synthase complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (leukocyte activation) AnnotationAssertion(Annotation( "GOC:add") "A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor.") @@ -74174,7 +73373,7 @@ AnnotationAssertion( "negative regulation of gluconeogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -74191,8 +73390,8 @@ AnnotationAssertion( "positive regulation of gluconeogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of cilium assembly) @@ -74296,7 +73495,6 @@ AnnotationAssertion( "negative regulation of DNA repair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -74313,7 +73511,6 @@ AnnotationAssertion( "positive regulation of DNA repair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -74391,19 +73588,20 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of cellular amino acid metabolic process) +# Class: (negative regulation of amino acid metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "down regulation of amino acid metabolic process") AnnotationAssertion( "down-regulation of amino acid metabolic process") AnnotationAssertion( "downregulation of amino acid metabolic process") AnnotationAssertion( "negative regulation of amino acid metabolism") AnnotationAssertion( "inhibition of amino acid metabolic process") AnnotationAssertion( "GO:0045763") -AnnotationAssertion(rdfs:label "negative regulation of cellular amino acid metabolic process") +AnnotationAssertion(rdfs:label "negative regulation of amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of amino acid metabolic process) @@ -74420,7 +73618,7 @@ AnnotationAssertion( "positive regulation of amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of angiogenesis) @@ -74576,6 +73774,7 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of glycogen catabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29024"^^xsd:anyURI) AnnotationAssertion( "down regulation of glycogen catabolic process") AnnotationAssertion( "down-regulation of glycogen catabolic process") AnnotationAssertion( "downregulation of glycogen catabolic process") @@ -74588,13 +73787,14 @@ AnnotationAssertion( "negative regulation of glycogen catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of glycogen catabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29024"^^xsd:anyURI) AnnotationAssertion( "positive regulation of glycogen breakdown") AnnotationAssertion( "positive regulation of glycogen catabolism") AnnotationAssertion( "positive regulation of glycogen degradation") @@ -74608,44 +73808,10 @@ AnnotationAssertion( "positive regulation of glycogen catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of glycolytic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.") -AnnotationAssertion( "down regulation of glycolysis") -AnnotationAssertion( "down-regulation of glycolysis") -AnnotationAssertion( "downregulation of glycolysis") -AnnotationAssertion( "inhibition of glycolysis") -AnnotationAssertion( "GO:0045820") -AnnotationAssertion(rdfs:label "negative regulation of glycolytic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of glycolytic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of glycolysis.") -AnnotationAssertion( "up regulation of glycolysis") -AnnotationAssertion( "up-regulation of glycolysis") -AnnotationAssertion( "upregulation of glycolysis") -AnnotationAssertion( "activation of glycolysis") -AnnotationAssertion( "stimulation of glycolysis") -AnnotationAssertion( "GO:0045821") -AnnotationAssertion(rdfs:label "positive regulation of glycolytic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (negative regulation of heart contraction) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction.") @@ -74706,7 +73872,6 @@ AnnotationAssertion( "negative regulation of isoprenoid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -74723,7 +73888,6 @@ AnnotationAssertion( "positive regulation of isoprenoid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -74931,6 +74095,37 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of translational termination) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination.") +AnnotationAssertion( "down regulation of translational termination") +AnnotationAssertion( "down-regulation of translational termination") +AnnotationAssertion( "downregulation of translational termination") +AnnotationAssertion( "inhibition of translational termination") +AnnotationAssertion( "GO:0045904") +AnnotationAssertion(rdfs:label "negative regulation of translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translational termination) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of translational termination.") +AnnotationAssertion( "up regulation of translational termination") +AnnotationAssertion( "up-regulation of translational termination") +AnnotationAssertion( "upregulation of translational termination") +AnnotationAssertion( "activation of translational termination") +AnnotationAssertion( "stimulation of translational termination") +AnnotationAssertion( "GO:0045905") +AnnotationAssertion(rdfs:label "positive regulation of translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (negative regulation of DNA recombination) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination.") @@ -75065,7 +74260,6 @@ AnnotationAssertion( "negative regulation of fatty acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -75083,7 +74277,6 @@ AnnotationAssertion( "positive regulation of fatty acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -75291,40 +74484,34 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of nucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleotides.") -AnnotationAssertion( "down regulation of nucleotide metabolic process") -AnnotationAssertion( "down-regulation of nucleotide metabolic process") -AnnotationAssertion( "downregulation of nucleotide metabolic process") -AnnotationAssertion( "negative regulation of nucleotide metabolism") -AnnotationAssertion( "inhibition of nucleotide metabolic process") -AnnotationAssertion( "GO:0045980") -AnnotationAssertion(rdfs:label "negative regulation of nucleotide metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of nucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleotides.") -AnnotationAssertion( "positive regulation of nucleotide metabolism") -AnnotationAssertion( "up regulation of nucleotide metabolic process") -AnnotationAssertion( "up-regulation of nucleotide metabolic process") -AnnotationAssertion( "upregulation of nucleotide metabolic process") -AnnotationAssertion( "activation of nucleotide metabolic process") -AnnotationAssertion( "stimulation of nucleotide metabolic process") -AnnotationAssertion( "GO:0045981") -AnnotationAssertion(rdfs:label "positive regulation of nucleotide metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of translational initiation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.") +AnnotationAssertion( "down regulation of translational initiation") +AnnotationAssertion( "down-regulation of translational initiation") +AnnotationAssertion( "downregulation of translational initiation") +AnnotationAssertion( "inhibition of translational initiation") +AnnotationAssertion( "GO:0045947") +AnnotationAssertion(rdfs:label "negative regulation of translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translational initiation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of translational initiation.") +AnnotationAssertion( "up regulation of translational initiation") +AnnotationAssertion( "up-regulation of translational initiation") +AnnotationAssertion( "upregulation of translational initiation") +AnnotationAssertion( "activation of translational initiation") +AnnotationAssertion( "stimulation of translational initiation") +AnnotationAssertion( "GO:0045948") +AnnotationAssertion(rdfs:label "positive regulation of translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of smooth muscle contraction) @@ -75425,36 +74612,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (ADP metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate.") -AnnotationAssertion( "ADP metabolism") -AnnotationAssertion( "GO:0046031") -AnnotationAssertion(rdfs:label "ADP metabolic process") -SubClassOf( ) -SubClassOf( ) - -# 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( "GO:0046032") -AnnotationAssertion(rdfs:label "ADP catabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - -# 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( "GO:0046034") -AnnotationAssertion(rdfs:label "ATP metabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (positive regulation of vitamin metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.") @@ -75495,45 +74652,49 @@ AnnotationAssertion( "GO:0046185") AnnotationAssertion(rdfs:label "aldehyde catabolic process") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) -# Class: (glucose import) +# Class: (D-glucose import) -AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of the hexose monosaccharide glucose into a cell or organelle.") +AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of the hexose monosaccharide D-glucose into a cell or organelle.") AnnotationAssertion( "Wikipedia:Glucose_uptake") +AnnotationAssertion( "glucose import") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "glucose uptake") AnnotationAssertion( "GO:0046323") -AnnotationAssertion(rdfs:label "glucose import") +AnnotationAssertion(rdfs:label "D-glucose import") SubClassOf( ) -# Class: (regulation of glucose import) +# Class: (regulation of D-glucose import) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.") +AnnotationAssertion( "regulation of glucose import") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "regulation of glucose uptake") AnnotationAssertion( "GO:0046324") -AnnotationAssertion(rdfs:label "regulation of glucose import") +AnnotationAssertion(rdfs:label "regulation of D-glucose import") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of glucose import) +# Class: (negative regulation of D-glucose import) AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.") AnnotationAssertion( "down regulation of glucose import") AnnotationAssertion( "down-regulation of glucose import") AnnotationAssertion( "downregulation of glucose import") +AnnotationAssertion( "negative regulation of glucose import") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "negative regulation of glucose uptake") AnnotationAssertion( "inhibition of glucose import") AnnotationAssertion( "GO:0046325") -AnnotationAssertion(rdfs:label "negative regulation of glucose import") +AnnotationAssertion(rdfs:label "negative regulation of D-glucose import") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (positive regulation of glucose import) +# Class: (positive regulation of D-glucose import) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that activates or increases the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.") +AnnotationAssertion( "positive regulation of glucose import") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "positive regulation of glucose uptake") AnnotationAssertion( "up regulation of glucose import") AnnotationAssertion( "up-regulation of glucose import") @@ -75541,7 +74702,7 @@ AnnotationAssertion( "activation of glucose import") AnnotationAssertion( "stimulation of glucose import") AnnotationAssertion( "GO:0046326") -AnnotationAssertion(rdfs:label "positive regulation of glucose import") +AnnotationAssertion(rdfs:label "positive regulation of D-glucose import") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -75572,25 +74733,6 @@ AnnotationAssertion(rdfs:label "carb SubClassOf( ) SubClassOf( ) -# Class: (organophosphate catabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the breakdown of organophosphates, any phosphate-containing organic compound.") -AnnotationAssertion( "organophosphate breakdown") -AnnotationAssertion( "organophosphate catabolism") -AnnotationAssertion( "organophosphate degradation") -AnnotationAssertion( "GO:0046434") -AnnotationAssertion(rdfs:label "organophosphate catabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (nicotinamide nucleotide metabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide.") -AnnotationAssertion( "nicotinamide nucleotide metabolism") -AnnotationAssertion( "GO:0046496") -AnnotationAssertion(rdfs:label "nicotinamide nucleotide metabolic process") -SubClassOf( ) - # Class: (saliva secretion) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "UBERON:0001836") "The regulated release of saliva from the salivary glands. In man, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin.") @@ -75858,7 +75000,7 @@ AnnotationAssertion( "GO:0046885") AnnotationAssertion(rdfs:label "regulation of hormone biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -75877,7 +75019,7 @@ AnnotationAssertion( "GO:0046886") AnnotationAssertion(rdfs:label "positive regulation of hormone biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -76001,6 +75143,17 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (pore complex) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20452"^^xsd:anyURI) +AnnotationAssertion( "pore") +AnnotationAssertion( "channel-forming toxin activity") +AnnotationAssertion( "pore-forming toxin activity") +AnnotationAssertion( "GO:0046930") +AnnotationAssertion(rdfs:label "pore complex") +SubClassOf( ) + # Class: (carboxylic acid transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).") @@ -76009,16 +75162,6 @@ AnnotationAssertion(rdfs:label "carb SubClassOf( ) SubClassOf( ) -# Class: (cellular ketone body metabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism.") -AnnotationAssertion( "cellular ketone body metabolism") -AnnotationAssertion( "GO:0046950") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular ketone body metabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (ketone body biosynthetic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetate and acetyl-CoA.") @@ -76028,9 +75171,7 @@ AnnotationAssertion( "ketone body synthesis") AnnotationAssertion( "GO:0046951") AnnotationAssertion(rdfs:label "ketone body biosynthetic process") -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -77082,7 +76223,7 @@ AnnotationAssertion( "regulation of enzyme activity") AnnotationAssertion( "regulation of metalloenzyme activity") AnnotationAssertion( "GO:0050790") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of catalytic activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -77585,7 +76726,6 @@ AnnotationAssertion( "GO:0050908") AnnotationAssertion(rdfs:label "detection of light stimulus involved in visual perception") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -78060,7 +77200,7 @@ AnnotationAssertion( "GO:0051174") AnnotationAssertion(rdfs:label "regulation of phosphorus metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of sulfur metabolic process) @@ -78076,7 +77216,7 @@ AnnotationAssertion( "GO:0051175") AnnotationAssertion(rdfs:label "negative regulation of sulfur metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -78094,7 +77234,7 @@ AnnotationAssertion( "GO:0051176") AnnotationAssertion(rdfs:label "positive regulation of sulfur metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -78416,7 +77556,7 @@ SubClassOf( "GOC:ai") "Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.") AnnotationAssertion( "hydrolase regulator") AnnotationAssertion( "GO:0051336") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of hydrolase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78427,7 +77567,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:ai") "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") AnnotationAssertion( "transferase regulator") AnnotationAssertion( "GO:0051338") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -78439,7 +77579,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:ai") "Any process that modulates the frequency, rate or extent of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.") AnnotationAssertion( "lyase regulator") AnnotationAssertion( "GO:0051339") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of lyase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78450,7 +77590,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:ai") "Any process that modulates the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6.") AnnotationAssertion( "ligase regulator") AnnotationAssertion( "GO:0051340") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of ligase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78461,7 +77601,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:ai") "Any process that modulates the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.") AnnotationAssertion( "oxidoreductase regulator") AnnotationAssertion( "GO:0051341") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of oxidoreductase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78477,7 +77617,7 @@ AnnotationAssertion( "activation of hydrolase activity") AnnotationAssertion( "stimulation of hydrolase activity") AnnotationAssertion( "GO:0051345") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of hydrolase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78493,7 +77633,7 @@ AnnotationAssertion( "hydrolase inhibitor") AnnotationAssertion( "inhibition of hydrolase activity") AnnotationAssertion( "GO:0051346") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of hydrolase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78510,7 +77650,7 @@ AnnotationAssertion( "activation of transferase activity") AnnotationAssertion( "stimulation of transferase activity") AnnotationAssertion( "GO:0051347") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "positive regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -78527,7 +77667,7 @@ AnnotationAssertion( "transferase inhibitor") AnnotationAssertion( "inhibition of transferase activity") AnnotationAssertion( "GO:0051348") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") AnnotationAssertion(rdfs:label "negative regulation of transferase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -78545,7 +77685,7 @@ AnnotationAssertion( "activation of lyase activity") AnnotationAssertion( "stimulation of lyase activity") AnnotationAssertion( "GO:0051349") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of lyase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78561,7 +77701,7 @@ AnnotationAssertion( "lyase inhibitor") AnnotationAssertion( "inhibition of lyase activity") AnnotationAssertion( "GO:0051350") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of lyase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78578,7 +77718,7 @@ AnnotationAssertion( "activation of ligase activity") AnnotationAssertion( "stimulation of ligase activity") AnnotationAssertion( "GO:0051351") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of ligase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78594,7 +77734,7 @@ AnnotationAssertion( "ligase inhibitor") AnnotationAssertion( "inhibition of ligase activity") AnnotationAssertion( "GO:0051352") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of ligase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78613,7 +77753,7 @@ AnnotationAssertion( "ribonucleotide reductase activating enzyme activity") AnnotationAssertion( "stimulation of oxidoreductase activity") AnnotationAssertion( "GO:0051353") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of oxidoreductase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78629,7 +77769,7 @@ AnnotationAssertion( "oxidoreductase inhibitor") AnnotationAssertion( "inhibition of oxidoreductase activity") AnnotationAssertion( "GO:0051354") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of oxidoreductase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -78884,7 +78024,7 @@ SubClassOf( ObjectSomeValuesFrom( (methylglyoxal catabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, the aldehyde of pyruvic acid.") -AnnotationAssertion( "MetaCyc:METHGLYUT-PWY") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28527"^^xsd:anyURI) AnnotationAssertion( "MetaCyc:Methylglyoxal-Detoxification") AnnotationAssertion( "methylglyoxal breakdown") AnnotationAssertion( "methylglyoxal catabolism") @@ -79586,21 +78726,6 @@ AnnotationAssertion(rdfs:label "tran SubClassOf( ) SubClassOf( ) -# Class: (nucleobase-containing small molecule metabolic process) - -AnnotationAssertion(Annotation( "GOC:vw") "The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.") -AnnotationAssertion( "nucleobase, nucleoside and nucleotide metabolism") -AnnotationAssertion( "nucleobase, nucleoside and nucleotide metabolic process") -AnnotationAssertion( "GO:0055086") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "nucleobase-containing small molecule metabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (regulation of cardiac muscle contraction) AnnotationAssertion(Annotation( "GOC:ecd") "Any process that modulates the frequency, rate or extent of cardiac muscle contraction.") @@ -79828,6 +78953,27 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of syncytium formation by plasma membrane fusion) + +AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.") +AnnotationAssertion( "GO:0060142") +AnnotationAssertion(rdfs:label "regulation of syncytium formation by plasma membrane fusion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of syncytium formation by plasma membrane fusion) + +AnnotationAssertion(Annotation( "GOC:dph") "Any process that increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.") +AnnotationAssertion( "GO:0060143") +AnnotationAssertion(rdfs:label "positive regulation of syncytium formation by plasma membrane fusion") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (milk ejection reflex) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:mr") Annotation( "GOC:st") "A reflex that occurs in response to suckling, beginning with a nerve impulse from a receptor in the mammary gland and ending with the ejection of milk from the gland. Signaling never reaches a level of consciousness.") @@ -79969,6 +79115,7 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -80867,6 +80014,33 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing complex assembly) + +AnnotationAssertion(Annotation( "GOC:jl") "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22580"^^xsd:anyURI) +AnnotationAssertion( "GO:0006461") +AnnotationAssertion( "GO:0034622") +AnnotationAssertion( "GO:0043623") +AnnotationAssertion( "cellular protein complex assembly") +AnnotationAssertion( "cellular macromolecule complex assembly") +AnnotationAssertion( "cellular protein-containing complex assembly") +AnnotationAssertion( "chaperone activity") +AnnotationAssertion( "macromolecular complex assembly") +AnnotationAssertion( "macromolecule complex assembly") +AnnotationAssertion( "protein complex assembly") +AnnotationAssertion( "protein complex formation") +AnnotationAssertion( "GO:0065003") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "protein-containing complex assembly") +SubClassOf( ) +SubClassOf( ) + # Class: (biological regulation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:mah") Annotation( "GOC:pr") Annotation( "GOC:vw") "Any process that modulates a measurable attribute of any biological process, quality or function.") @@ -80892,7 +80066,7 @@ SubClassOf( "GOC:isa_complete") "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.") AnnotationAssertion( "regulation of a molecular function") AnnotationAssertion( "GO:0065009") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of molecular function") @@ -80972,6 +80146,17 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (mitochondrial translational initiation) + +AnnotationAssertion(Annotation( "GOC:mah") "The process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA.") +AnnotationAssertion(Annotation( "GOC:mah") "mitochondrial translation initiation") +AnnotationAssertion( "GO:0070124") +AnnotationAssertion(rdfs:label "mitochondrial translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (mitochondrial translational elongation) AnnotationAssertion(Annotation( "GOC:mah") "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in a mitochondrion.") @@ -80983,6 +80168,17 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (mitochondrial translational termination) + +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "http://mitogenome.org/index.php/Genetic_Code_of_mitochondria") "The process resulting in the release of a polypeptide chain from the ribosome in a mitochondrion, usually in response to a termination codon (note that mitochondria use variants of the universal genetic code that differ between different taxa).") +AnnotationAssertion(Annotation( "GOC:mah") "mitochondrial translation termination") +AnnotationAssertion( "GO:0070126") +AnnotationAssertion(rdfs:label "mitochondrial translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of mitochondrial translation) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion.") @@ -81025,6 +80221,40 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of mitochondrial translational initiation) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion.") +AnnotationAssertion(Annotation( "GOC:mah") "regulation of mitochondrial translation initiation") +AnnotationAssertion( "GO:0070132") +AnnotationAssertion(rdfs:label "regulation of mitochondrial translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of mitochondrial translational initiation) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion.") +AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of mitochondrial translation initiation") +AnnotationAssertion( "GO:0070133") +AnnotationAssertion(rdfs:label "negative regulation of mitochondrial translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of mitochondrial translational initiation) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion.") +AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of mitochondrial translation initiation") +AnnotationAssertion( "GO:0070134") +AnnotationAssertion(rdfs:label "positive regulation of mitochondrial translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (anchoring junction) AnnotationAssertion(Annotation( "ISBN:0815332181") "A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix.") @@ -81310,28 +80540,6 @@ AnnotationAssertion(rdfs:label "prol SubClassOf( ) SubClassOf( ) -# Class: (respirasome) - -AnnotationAssertion(Annotation( "GOC:ecd") Annotation( "GOC:mah") Annotation( "ISBN:0198547684") Annotation( "Wikipedia:Respirasome") "The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/12846"^^xsd:anyURI) -AnnotationAssertion(Annotation( "GOC:mah") "membrane electron transport chain") -AnnotationAssertion( "respiratory chain") -AnnotationAssertion( "GO:0070469") -AnnotationAssertion(rdfs:label "respirasome") -SubClassOf( ) - -# Class: (plasma membrane respirasome) - -AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:imk") Annotation( "GOC:mah") Annotation( "ISBN:0198547684") "A respiratory chain located in the plasma membrane of a cell; made up of the protein complexes that form the electron transport system (the respiratory chain), associated with the plasma membrane. The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/12846"^^xsd:anyURI) -AnnotationAssertion(Annotation( "GOC:mah") "plasma membrane electron transport chain") -AnnotationAssertion( "plasma membrane respiratory chain") -AnnotationAssertion( "GO:0070470") -AnnotationAssertion(rdfs:label "plasma membrane respirasome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (response to oxygen levels) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen.") @@ -81454,7 +80662,6 @@ AnnotationAssertion( "regulation of bile acid biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -81475,7 +80682,6 @@ AnnotationAssertion( "negative regulation of bile acid biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -81497,7 +80703,6 @@ AnnotationAssertion( "positive regulation of bile acid biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -81523,7 +80728,6 @@ AnnotationAssertion( "negative regulation of glycogen metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -81538,7 +80742,6 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -81885,7 +81088,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mah") "The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") AnnotationAssertion( "2010-03-08T03:56:28Z") AnnotationAssertion( "GO:0071705") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nitrogen compound transport") SubClassOf( ) @@ -82029,6 +81232,19 @@ AnnotationAssertion(rdfs:label "IgM SubClassOf( ) SubClassOf( ) +# Class: (protein-RNA complex organization) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25143"^^xsd:anyURI) +AnnotationAssertion( "2010-09-08T10:10:35Z") +AnnotationAssertion(Annotation( "GOC:mah") "RNA-protein complex subunit organization") +AnnotationAssertion(Annotation( "GOC:mah") "protein-RNA complex subunit organization") +AnnotationAssertion(Annotation( "GOC:mah") "ribonucleoprotein complex subunit organisation") +AnnotationAssertion( "ribonucleoprotein complex subunit organization") +AnnotationAssertion( "GO:0071826") +AnnotationAssertion(rdfs:label "protein-RNA complex organization") +SubClassOf( ) + # Class: (cellular component organization or biogenesis) AnnotationAssertion(Annotation( "GOC:mah") "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.") @@ -82183,52 +81399,6 @@ AnnotationAssertion(rdfs:label "bloo SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (purine-containing compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof.") -AnnotationAssertion( "2011-01-04T03:03:59Z") -AnnotationAssertion( "purine and derivative metabolic process") -AnnotationAssertion(Annotation( "GOC:mah") "purine-containing compound metabolism") -AnnotationAssertion( "GO:0072521") -AnnotationAssertion(rdfs:label "purine-containing compound metabolic process") -SubClassOf( ) - -# Class: (purine-containing compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the breakdown of a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof.") -AnnotationAssertion( "2011-01-04T03:17:20Z") -AnnotationAssertion( "purine and derivative catabolic process") -AnnotationAssertion(Annotation( "GOC:mah") "purine-containing compound breakdown") -AnnotationAssertion(Annotation( "GOC:mah") "purine-containing compound catabolism") -AnnotationAssertion(Annotation( "GOC:mah") "purine-containing compound degradation") -AnnotationAssertion( "GO:0072523") -AnnotationAssertion(rdfs:label "purine-containing compound catabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (pyridine-containing compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof.") -AnnotationAssertion( "2011-01-04T03:21:47Z") -AnnotationAssertion( "pyridine and derivative metabolic process") -AnnotationAssertion(Annotation( "GOC:mah") "pyridine-containing compound metabolism") -AnnotationAssertion( "GO:0072524") -AnnotationAssertion(rdfs:label "pyridine-containing compound metabolic process") -SubClassOf( ) - -# Class: (pyridine-containing compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the breakdown of a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof.") -AnnotationAssertion( "2011-01-04T03:23:14Z") -AnnotationAssertion( "pyridine and derivative catabolic process") -AnnotationAssertion(Annotation( "GOC:mah") "pyridine-containing compound breakdown") -AnnotationAssertion(Annotation( "GOC:mah") "pyridine-containing compound catabolism") -AnnotationAssertion(Annotation( "GOC:mah") "pyridine-containing compound degradation") -AnnotationAssertion( "GO:0072526") -AnnotationAssertion(rdfs:label "pyridine-containing compound catabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (reactive oxygen species metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.") @@ -82237,7 +81407,7 @@ AnnotationAssertion(Annotation( "GOC:mah") "reactive oxygen species metabolism") AnnotationAssertion( "GO:0072593") AnnotationAssertion(rdfs:label "reactive oxygen species metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (regulation of primary metabolic process) @@ -82720,6 +81890,19 @@ AnnotationAssertion(rdfs:label "amel SubClassOf( ) SubClassOf( ) +# Class: (apoptotic signaling pathway) + +AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.") +AnnotationAssertion( "2011-11-23T09:30:23Z") +AnnotationAssertion( "GO:0008624") +AnnotationAssertion(Annotation( "GOC:mah") "apoptotic signalling pathway") +AnnotationAssertion( "induction of apoptosis by extracellular signals") +AnnotationAssertion( "GO:0097190") +AnnotationAssertion(rdfs:comment "This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways.") +AnnotationAssertion(rdfs:label "apoptotic signaling pathway") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (execution phase of apoptosis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:21760595") "A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.") @@ -82787,6 +81970,18 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (ciliary basal body-plasma membrane docking) + +AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:13978319") Annotation( "PMID:23348840") Annotation( "PMID:23530209") Annotation( "PMID:25686250") Annotation( "PMID:26981235") "The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.") +AnnotationAssertion( "2016-08-05T16:12:33Z") +AnnotationAssertion( "ciliary basal body docking") +AnnotationAssertion( "anchoring of the basal body to the plasma membrane") +AnnotationAssertion( "GO:0097711") +AnnotationAssertion(rdfs:comment "Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella.") +AnnotationAssertion(rdfs:label "ciliary basal body-plasma membrane docking") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (vesicle targeting, trans-Golgi to periciliary membrane compartment) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:20106869") Annotation( "PMID:23351793") Annotation( "PMID:24814148") Annotation( "PMID:26485645") "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces.") @@ -82859,6 +82054,14 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (mucin granule) + +AnnotationAssertion(Annotation( "PMID:16377632") "A secretory granule that contains mucin.") +AnnotationAssertion( "2014-03-11T15:59:11Z") +AnnotationAssertion( "GO:0098594") +AnnotationAssertion(rdfs:label "mucin granule") +SubClassOf( ) + # Class: (cell-cell adhesion) AnnotationAssertion(Annotation( "GOC:dos") "The attachment of one cell to another cell via adhesion molecules.") @@ -82994,16 +82197,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (inner mitochondrial membrane protein complex) - -AnnotationAssertion(Annotation( "GOC:dos") "Any protein complex that is part of the inner mitochondrial membrane.") -AnnotationAssertion( "GO:0098800") -AnnotationAssertion(rdfs:label "inner mitochondrial membrane protein complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of renal system process) AnnotationAssertion(Annotation( "GOC:dos") "Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system.") @@ -83023,15 +82216,6 @@ AnnotationAssertion(rdfs:label "plas SubClassOf( ) SubClassOf( ) -# Class: (respiratory chain complex) - -AnnotationAssertion(Annotation( "GOC:dos") "Any protein complex that is part of a respiratory chain.") -AnnotationAssertion( "GO:0098803") -AnnotationAssertion(rdfs:label "respiratory chain complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (nuclear chromosome segregation) AnnotationAssertion(Annotation( "GOC:dos") "The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.") @@ -83266,7 +82450,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:dos") "The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission.") AnnotationAssertion( "GO:0099531") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "presynaptic process involved in chemical synaptic transmission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -83509,16 +82693,18 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (cellular anatomical entity) +# Class: (cellular anatomical structure) -AnnotationAssertion(Annotation( "GOC:kmv") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion(Annotation( "GOC:kmv") "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24200"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28978"^^xsd:anyURI) AnnotationAssertion( "2019-08-12T18:01:37Z") +AnnotationAssertion( "cellular anatomical entity") AnnotationAssertion( "GO:0110165") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular anatomical entity") +AnnotationAssertion(rdfs:label "cellular anatomical structure") SubClassOf( ) # Class: (plasma membrane bounded cell projection) @@ -83750,6 +82936,16 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (organelle localization by membrane tethering) + +AnnotationAssertion(Annotation( "PMID:27875684") "The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other.") +AnnotationAssertion( "2017-06-27T09:58:51Z") +AnnotationAssertion( "GO:0140056") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "organelle localization by membrane tethering") +SubClassOf( ) +SubClassOf( ) + # Class: (extracellular vesicle biogenesis) AnnotationAssertion(Annotation( "PMID:28736435") "The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content.") @@ -83881,6 +83077,18 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (cell-cell fusion) + +AnnotationAssertion(Annotation( "Wikipedia:Cell_fusion") "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15939"^^xsd:anyURI) +AnnotationAssertion( "2018-08-13T18:38:18Z") +AnnotationAssertion( "cell fusion") +AnnotationAssertion( "cell cell fusion") +AnnotationAssertion( "GO:0140253") +AnnotationAssertion(rdfs:label "cell-cell fusion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (export from cell) AnnotationAssertion(Annotation( "GOC:pg") "The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis.") @@ -83973,7 +83181,6 @@ AnnotationAssertion( "proteinogenic amino acid metabolic process") SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (regulation of cytokine production involved in inflammatory response) @@ -84314,79 +83521,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of purine nucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of purine nucleotide metabolic process.") -AnnotationAssertion( "2012-05-11T05:43:15Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of purine metabolism") -AnnotationAssertion( "GO:1900542") -AnnotationAssertion(rdfs:label "regulation of purine nucleotide metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of purine nucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of purine nucleotide metabolic process.") -AnnotationAssertion( "2012-05-11T05:44:21Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of purine nucleotide metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of purine nucleotide metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of purine nucleotide metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of purine metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of purine metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of purine metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of purine metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of purine nucleotide metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of purine metabolism") -AnnotationAssertion( "GO:1900543") -AnnotationAssertion(rdfs:label "negative regulation of purine nucleotide metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of purine nucleotide metabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of purine nucleotide metabolic process.") -AnnotationAssertion( "2012-05-11T05:44:43Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of purine nucleotide metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of purine nucleotide metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of purine nucleotide metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of purine metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of purine nucleotide metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of purine nucleotide metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of purine metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of purine metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of purine metabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of purine metabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of purine metabolism") -AnnotationAssertion( "GO:1900544") -AnnotationAssertion(rdfs:label "positive regulation of purine nucleotide metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (carbohydrate derivative metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways involving carbohydrate derivative.") @@ -84400,18 +83534,6 @@ AnnotationAssertion( "carbohydrate derivative metabolic process") SubClassOf( ) -# Class: (carbohydrate derivative catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative.") -AnnotationAssertion( "2012-07-12T04:05:31Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "carbohydrate derivative breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "carbohydrate derivative catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "carbohydrate derivative degradation") -AnnotationAssertion( "GO:1901136") -AnnotationAssertion(rdfs:label "carbohydrate derivative catabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (carbohydrate derivative biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the formation of carbohydrate derivative.") @@ -84437,18 +83559,57 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (nucleoside phosphate catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the breakdown of a nucleoside phosphate.") -AnnotationAssertion( "2012-08-20T12:33:25Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "nucleoside phosphate breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "nucleoside phosphate catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "nucleoside phosphate degradation") -AnnotationAssertion( "GO:1901292") -AnnotationAssertion(rdfs:label "nucleoside phosphate catabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) +# Class: (regulation of formation of translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex.") +AnnotationAssertion( "2012-07-25T02:26:58Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of translation initiation ternary complex assembly") +AnnotationAssertion( "GO:1901190") +AnnotationAssertion(rdfs:label "regulation of formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of formation of translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex.") +AnnotationAssertion( "2012-07-25T02:27:21Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of formation of translation initiation ternary complex") +AnnotationAssertion( "GO:1901191") +AnnotationAssertion(rdfs:label "negative regulation of formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of formation of translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex.") +AnnotationAssertion( "2012-07-25T02:27:29Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of formation of translation initiation ternary complex") +AnnotationAssertion( "GO:1901192") +AnnotationAssertion(rdfs:label "positive regulation of formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of flagellated sperm motility) @@ -84659,46 +83820,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (organonitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways involving organonitrogen compound.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "2012-11-04T15:17:52Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound metabolism") -AnnotationAssertion( "GO:1901564") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organonitrogen compound metabolic process") -SubClassOf( ) - -# Class: (organonitrogen compound catabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "2012-11-04T15:17:56Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound breakdown") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound degradation") -AnnotationAssertion( "GO:1901565") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organonitrogen compound catabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (organonitrogen compound biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the formation of organonitrogen compound.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "2012-11-04T15:18:00Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound anabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound biosynthesis") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound synthesis") -AnnotationAssertion( "GO:1901566") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organonitrogen compound biosynthetic process") -SubClassOf( ) -SubClassOf( ) - # Class: (fatty acid derivative metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways involving fatty acid derivative.") @@ -84730,7 +83851,6 @@ AnnotationAssertion( "alpha-amino acid metabolic process") SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (organic hydroxy compound metabolic process) @@ -85082,11 +84202,13 @@ SubClassOf( ObjectSomeValuesFrom( (ketone body metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways involving ketone body.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22938"^^xsd:anyURI) AnnotationAssertion( "2013-06-13T10:37:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "ketone body metabolism") AnnotationAssertion( "GO:1902224") AnnotationAssertion(rdfs:label "ketone body metabolic process") SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (apoptotic process involved in blood vessel morphogenesis) @@ -85272,15 +84394,6 @@ AnnotationAssertion( "catalytic complex") SubClassOf( ) -# Class: (transmembrane transporter complex) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "PMID:18024586") "A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other.") -AnnotationAssertion( "2013-11-13T16:23:04Z") -AnnotationAssertion( "GO:1902495") -AnnotationAssertion(rdfs:label "transmembrane transporter complex") -SubClassOf( ) -SubClassOf( ) - # Class: (regulation of intracellular signal transduction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:signaling") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of intracellular signal transduction.") @@ -86270,57 +85383,6 @@ SubClassOf( ) SubClassOf( 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( "2014-10-30T19:04:24Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATP metabolism") -AnnotationAssertion( "GO:1903578") -AnnotationAssertion(rdfs:label "regulation of ATP metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( 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( "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( "GO:1903579") -AnnotationAssertion(rdfs:label "negative regulation of ATP metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( 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( "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( "GO:1903580") -AnnotationAssertion(rdfs:label "positive regulation of ATP metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of hemopoiesis) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:20080761") "Any process that modulates the frequency, rate or extent of hemopoiesis.") @@ -86500,7 +85562,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of oryzatym") AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of sumiklat") AnnotationAssertion( "GO:1903770") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of beta-galactosidase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -86580,7 +85642,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of oryzatym") AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of sumiklat") AnnotationAssertion( "GO:1903771") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of beta-galactosidase activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -86786,6 +85848,7 @@ AnnotationAssertion(Annotation( "2015-03-27T16:09:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein amino acid O-linked glycosylation") AnnotationAssertion( "GO:1904098") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of protein O-linked glycosylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -86805,6 +85868,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of protein O-linked glycosylation") AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of protein amino acid O-linked glycosylation") AnnotationAssertion( "GO:1904099") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of protein O-linked glycosylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -86825,6 +85889,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of protein O-linked glycosylation") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of protein amino acid O-linked glycosylation") AnnotationAssertion( "GO:1904100") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of protein O-linked glycosylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -86903,7 +85968,6 @@ AnnotationAssertion( "regulation of bile acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -86923,7 +85987,6 @@ AnnotationAssertion(Annotation( "GO:1904252") AnnotationAssertion(rdfs:label "negative regulation of bile acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -86945,7 +86008,6 @@ AnnotationAssertion(Annotation( "GO:1904253") AnnotationAssertion(rdfs:label "positive regulation of bile acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -87237,14 +86299,15 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (glucose transmembrane transport) +# Class: (D-glucose transmembrane transport) -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000069") Annotation( "PMID:9090050") "The process in which glucose is transported across a membrane.") +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000069") Annotation( "PMID:9090050") "The process in which D-glucose is transported across a membrane.") AnnotationAssertion( "2015-09-04T17:20:16Z") AnnotationAssertion( "GO:0015758") +AnnotationAssertion( "glucose transmembrane transport") AnnotationAssertion( "glucose transport") AnnotationAssertion( "GO:1904659") -AnnotationAssertion(rdfs:label "glucose transmembrane transport") +AnnotationAssertion(rdfs:label "D-glucose transmembrane transport") SubClassOf( ) # Class: (regulation of somatic stem cell division) @@ -87721,7 +86784,6 @@ AnnotationAssertion( "regulation of membrane lipid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of mitochondrial translational elongation) @@ -88445,15 +87507,6 @@ AnnotationAssertion( "neutrophil migration") SubClassOf( ) -# Class: (transporter complex) - -AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:15449578") "A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells.") -AnnotationAssertion( "2014-03-26T14:23:27Z") -AnnotationAssertion( "GO:1990351") -AnnotationAssertion(rdfs:comment "An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay).") -AnnotationAssertion(rdfs:label "transporter complex") -SubClassOf( ) - # Class: (small intestine smooth muscle contraction) AnnotationAssertion(Annotation( "PMID:11991626") "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry in the intestine between the stomach and the large intestine.") @@ -88820,7 +87873,7 @@ AnnotationAssertion( AnnotationAssertion( "negative regulation of receptor activity") AnnotationAssertion( "negative regulation of signalling receptor activity") AnnotationAssertion( "GO:2000272") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "negative regulation of signaling receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -88833,7 +87886,7 @@ AnnotationAssertion(Annotation( "2010-12-02T09:28:50Z") AnnotationAssertion( "positive regulation of signalling receptor activity") AnnotationAssertion( "GO:2000273") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of signaling receptor activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -88884,7 +87937,7 @@ AnnotationAssertion(Annotation( "GO:2000377") AnnotationAssertion(rdfs:label "regulation of reactive oxygen species metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of reactive oxygen species metabolic process) @@ -88896,7 +87949,7 @@ AnnotationAssertion(Annotation( "GO:2000378") AnnotationAssertion(rdfs:label "negative regulation of reactive oxygen species metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -88909,7 +87962,7 @@ AnnotationAssertion(Annotation( "GO:2000379") AnnotationAssertion(rdfs:label "positive regulation of reactive oxygen species metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -89019,7 +88072,6 @@ AnnotationAssertion( AnnotationAssertion( "GO:2000609") AnnotationAssertion(rdfs:label "regulation of thyroid hormone generation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -89030,7 +88082,6 @@ AnnotationAssertion( AnnotationAssertion( "GO:2000610") AnnotationAssertion(rdfs:label "negative regulation of thyroid hormone generation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -89042,7 +88093,6 @@ AnnotationAssertion( AnnotationAssertion( "GO:2000611") AnnotationAssertion(rdfs:label "positive regulation of thyroid hormone generation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -89521,6 +88571,44 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of apoptotic signaling pathway) + +AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that modulates the frequency, rate or extent of apoptotic signaling pathway.") +AnnotationAssertion( "2011-11-24T01:20:49Z") +AnnotationAssertion(Annotation( "GOC:mah") "regulation of apoptotic signalling pathway") +AnnotationAssertion( "GO:2001233") +AnnotationAssertion(rdfs:label "regulation of apoptotic signaling pathway") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of apoptotic signaling pathway) + +AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway.") +AnnotationAssertion( "2011-11-24T01:20:54Z") +AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of apoptotic signalling pathway") +AnnotationAssertion( "GO:2001234") +AnnotationAssertion(rdfs:label "negative regulation of apoptotic signaling pathway") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of apoptotic signaling pathway) + +AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.") +AnnotationAssertion( "2011-11-24T01:20:58Z") +AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of apoptotic signalling pathway") +AnnotationAssertion( "GO:2001235") +AnnotationAssertion(rdfs:label "positive regulation of apoptotic signaling pathway") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (negative regulation of chromosome organization) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization.") @@ -90811,7 +89899,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "concentration of") -SubClassOf( ) +SubClassOf( ) # Class: (frequency) @@ -90905,6 +89993,7 @@ SubClassOf( (qualitative) +AnnotationAssertion(Annotation( "https://libguides.macalester.edu/c.php?g=527786&p=3608639") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK470395/") "A quality of an entity that is descriptive or observational, typically not represented numerically.") AnnotationAssertion( "PATO:0000068") AnnotationAssertion(rdfs:comment "TODO: define this or obsolete it and move children somewhere else.") AnnotationAssertion(rdfs:label "qualitative") @@ -90934,7 +90023,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term was originally named \"presence\". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.") AnnotationAssertion(rdfs:label "amount") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (rhythm quality) @@ -91125,7 +90214,6 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "arrested") SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mobile) @@ -91212,7 +90300,7 @@ AnnotationAssertion( "increased frequency") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (decreased frequency) @@ -91225,7 +90313,7 @@ AnnotationAssertion( "decreased frequency") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (hard) @@ -92413,6 +91501,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "increased concentration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -92426,6 +91515,7 @@ AnnotationAssertion( "decreased concentration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (dense) @@ -92745,16 +91835,6 @@ AnnotationAssertion( "anucleate") SubClassOf( ) -# Class: (binucleate) - -AnnotationAssertion(Annotation( "Biology-online:Biology-online") "A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.") -AnnotationAssertion( "PATO:0001406") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "binucleate") -SubClassOf( ) - # Class: (mononucleate) AnnotationAssertion(Annotation( "Biology-online:Biology-online") "A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.") @@ -92765,13 +91845,13 @@ AnnotationAssertion( "mononucleate") SubClassOf( ) -# Class: (ciliatedness) +# Class: (ciliated) -AnnotationAssertion(Annotation( "Wikipedia:http://en.wikipedia.org/wiki/Ciliated") "A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body.") +AnnotationAssertion(Annotation( "PMID:36924208") Annotation( "wikipedia:Cilium") "A cellular quality inhering in a bearer by virtue of the bearer's having one or more cilia as a part.") AnnotationAssertion( "PATO:0001408") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "ciliatedness") +AnnotationAssertion(rdfs:label "ciliated") SubClassOf( ) # Class: (spindle-shaped) @@ -93290,8 +92370,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has number of") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (lacking processual parts) @@ -93932,6 +93011,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "increased diameter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (decreased diameter) @@ -93941,6 +93021,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "decreased diameter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (liquid configuration) @@ -94302,6 +93383,7 @@ AnnotationAssertion( "decreased acidity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (increased acidity) @@ -94312,6 +93394,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "increased acidity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -94358,7 +93441,7 @@ SubClassOf( ObjectSomeValuesFrom( (dislocated) -AnnotationAssertion(Annotation( "thefreedictionary.com:thefreedictionary.com") "A positional quality inhering in a bearer by virtue of the bearer's being out of its usual or proper place, or position.") +AnnotationAssertion(Annotation( "thefreedictionary.com:thefreedictionary.com") "A positional quality inhering in a bearer by virtue of the bearer's being out of its usual or proper place, or position due to it being physically moved from the normal location.") AnnotationAssertion( "PATO:0001479") AnnotationAssertion( "PATO:0002158") AnnotationAssertion( "PATO:0002159") @@ -94704,6 +93787,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "decreased variability of size") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (increased variability of size) @@ -94713,6 +93798,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "increased variability of size") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (cuspidate) @@ -94823,6 +93910,7 @@ AnnotationAssertion( "Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type.") AnnotationAssertion(rdfs:label "has fewer parts of type") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -94840,6 +93928,7 @@ AnnotationAssertion( "In polydactyly, the bearer of the quality is the hand, and the entity type being counted is 'finger'. In EQ syntax, E=hand, Q= E2=finger.") AnnotationAssertion(rdfs:label "has extra parts of type") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -95467,17 +94556,6 @@ AnnotationAssertion( "displaced") SubClassOf( ) -# Class: (molecular quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.") -AnnotationAssertion( ) -AnnotationAssertion( "2010-03-10T03:18:15Z") -AnnotationAssertion( "PATO:0002061") -AnnotationAssertion( "relational molecular quality") -AnnotationAssertion( "PATO:0002182") -AnnotationAssertion(rdfs:label "molecular quality") -SubClassOf( ) - # Class: (quality of a substance) AnnotationAssertion(Annotation( "PATOC:GVG") "A quality inhering in a bearer by virtue of its constitution.") @@ -95639,8 +94717,10 @@ SubClassOf( (aplastic/hypoplastic) +AnnotationAssertion(Annotation( "https://orcid.org/0000-0003-4606-0597") "Decreased size or absence of organ, tissue or cell due to a reduction in cell numbers.") AnnotationAssertion( ) AnnotationAssertion( "2011-04-18T05:11:33Z") +AnnotationAssertion( "aplasia/hypoplasia") AnnotationAssertion( "PATO:0002290") AnnotationAssertion(rdfs:label "aplastic/hypoplastic") SubClassOf( ) @@ -95696,6 +94776,7 @@ AnnotationAssertion( "increased quality") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (decreased quality) @@ -95706,6 +94787,7 @@ AnnotationAssertion( "decreased quality") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (decreased process quality) @@ -96023,7 +95105,7 @@ SubClassOf( (cell morphology) -AnnotationAssertion(Annotation( "ORCID:0000-0002-7073-9172") "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure.") +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-7073-9172") "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure.") AnnotationAssertion( ) AnnotationAssertion( "2021-01-23T11:31:53Z") AnnotationAssertion( "PATO:0010006") @@ -96031,6 +95113,15 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "cell morphology") SubClassOf( ) +# Class: (multiciliated) + +AnnotationAssertion(Annotation( "PMID:36924208") "A cellular quality inhering in a bearer by virtue of the bearer's having multiple cilia.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-07-23T10:43:20Z"^^xsd:dateTime) +AnnotationAssertion( "PATO:0010007") +AnnotationAssertion(rdfs:label "multiciliated") +SubClassOf( ) + # Class: (absence due to degeneration) AnnotationAssertion(Annotation( "PATOC:PortlandMeetingFeb2015") "Absence due to a degenerative process.") @@ -96120,6 +95211,8 @@ AnnotationAssertion( "Example: decreased proportion of CD4 T cells relative to total T cells.") AnnotationAssertion(rdfs:label "decreased ratio") EquivalentClasses( ObjectIntersectionOf( )) +SubClassOf( ) +SubClassOf( ) # Class: (increased ratio) @@ -96134,6 +95227,8 @@ AnnotationAssertion( "Example: increased proportion of CD4 T cells relative to total T cells.") AnnotationAssertion(rdfs:label "increased ratio") EquivalentClasses( ObjectIntersectionOf( )) +SubClassOf( ) +SubClassOf( ) # Class: (fragmented) @@ -96203,6 +95298,7 @@ AnnotationAssertion( "normal object quality") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (normal acidity) @@ -96511,6 +95607,7 @@ AnnotationAssertion( "normal diameter") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (normal anterior-posterior diameter) @@ -96646,6 +95743,7 @@ AnnotationAssertion( "normal process quality") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (normal variability of size) @@ -96656,6 +95754,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "normal variability of size") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (normal viscosity) @@ -96726,6 +95826,7 @@ AnnotationAssertion( "PATO:0055003") AnnotationAssertion(rdfs:label "increased rate of occurrence") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (decreased rate of occurrence) @@ -96736,6 +95837,7 @@ AnnotationAssertion( "PATO:0055004") AnnotationAssertion(rdfs:label "decreased rate of occurrence") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (cortical bipolar morphology) @@ -96795,13 +95897,20 @@ AnnotationAssertion( "quality of interaction of a substance with electromagnetic radiation") SubClassOf( ) +# Class: (quantitative) + +AnnotationAssertion(Annotation( "https://libguides.macalester.edu/c.php?g=527786&p=3608639") Annotation( "https://www.nnlm.gov/guides/data-glossary/quantitative-data") "A quality of an entity that can be represented numerically, including anything that can be counted, measured, or given a numerical value.") +AnnotationAssertion( "PATO:0103000") +AnnotationAssertion(rdfs:label "quantitative") +SubClassOf( ) + # Class: (protein) AnnotationAssertion(Annotation( "PRO:DAN") Annotation( "PRO:WCB") "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.") AnnotationAssertion(Annotation( "PRO:DAN") "natural protein") AnnotationAssertion(Annotation( "IEDB:BP") "native protein") AnnotationAssertion( "PR:000000001") -AnnotationAssertion(rdfs:comment "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:comment "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( ) @@ -99500,6 +98609,15 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein phosphatase C isoform CD45R") SubClassOf( ) +# Class: (obsolete protein-containing material entity) + +AnnotationAssertion(Annotation( "PRO:DAN") "OBSOLETE. A material entity that minimally consists of a protein.") +AnnotationAssertion( "PR:000064867") +AnnotationAssertion( "PR:000050567") +AnnotationAssertion(rdfs:comment "Note: Made obsolete since the term definition was much broader than intended. Originally meant to include only single proteins (and derivatives thereof; PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566), it instead also included cells defined as having certain protein attachments.") +AnnotationAssertion(rdfs:label "obsolete protein-containing material entity") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) + # Class: (protein-containing molecular entity) AnnotationAssertion(Annotation( "PRO:DAN") "A molecular entity that minimally consists of a protein.") @@ -99632,7 +98750,6 @@ SubClassOf( "A material entity consisting of multiple components that are causally integrated.") AnnotationAssertion(rdfs:label "system") -SubClassOf( ) # Class: (processual entity) @@ -100387,7 +99504,6 @@ AnnotationAssertion( "WBbt:0005739") AnnotationAssertion( "Wikipedia:Head") AnnotationAssertion( "XAO:0003024") -AnnotationAssertion( "ZFA:0001114") AnnotationAssertion( "galen:Head") AnnotationAssertion(Annotation( "FMA:7154") "head (volume)") AnnotationAssertion( "adult head") @@ -100557,6 +99673,7 @@ AnnotationAssertion(Annotation( "MESH:A09.246.631.909.625.125") "acoustic macula") AnnotationAssertion(Annotation( "MESH:A09.246.631.909.625.125") Annotation( ) "acoustic maculae") AnnotationAssertion( "UBERON:0000054") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macula") @@ -100854,7 +99971,6 @@ AnnotationAssertion( "UBERON:0000066") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fully formed stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -100880,7 +99996,6 @@ AnnotationAssertion( "embryogenesis") AnnotationAssertion( "UBERON:0000068") AnnotationAssertion(rdfs:label "embryo stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -100896,7 +100011,6 @@ AnnotationAssertion( "UBERON:0000071") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "death stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -101331,7 +100445,6 @@ AnnotationAssertion( "postembryonic") AnnotationAssertion( "UBERON:0000092") AnnotationAssertion(rdfs:label "post-embryonic stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -101432,7 +100545,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "life cycle") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -101488,7 +100600,6 @@ AnnotationAssertion(Annotation( "UBERON:0000106") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "zygote stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -101512,7 +100623,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cleavage stage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -101536,7 +100646,6 @@ AnnotationAssertion( "UBERON:0000108") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blastula stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -101564,7 +100673,6 @@ AnnotationAssertion(Annotation( "UBERON:0000109") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "gastrula stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -101580,7 +100688,6 @@ AnnotationAssertion( "XAO:1000006") AnnotationAssertion( "UBERON:0000110") AnnotationAssertion(rdfs:label "neurula stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -101599,7 +100706,6 @@ AnnotationAssertion( "segmentation stage") AnnotationAssertion( "UBERON:0000111") AnnotationAssertion(rdfs:label "organogenesis stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -101621,7 +100727,6 @@ AnnotationAssertion(Annotation( "UBERON:0000112") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sexually immature stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -101640,7 +100745,6 @@ AnnotationAssertion( "ZFS:0000044") AnnotationAssertion( "UBERON:0000113") AnnotationAssertion(rdfs:label "post-juvenile adult stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -104208,7 +103312,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "material anatomical entity") -SubClassOf( ) SubClassOf( ) DisjointClasses( ) @@ -104230,7 +103333,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "immaterial anatomical entity") -SubClassOf( ) SubClassOf( ) # Class: (anatomical system) @@ -106500,7 +105602,7 @@ AnnotationAssertion( "ZFA:0000560") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "ovarian duct") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "ovarian tube") -AnnotationAssertion( "uterine tube") +AnnotationAssertion( "uterine tube") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "female reproductive tracts") AnnotationAssertion(Annotation( "ZFA:0000560") Annotation( ) "oviducts") AnnotationAssertion(Annotation( "BTO:0000980") "tuba uterina") @@ -106948,7 +106050,6 @@ AnnotationAssertion( "Wikipedia:Circulatory_system") AnnotationAssertion(Annotation( "Wikipedia:Circulatory_system") Annotation( ) "systema cardiovasculare") AnnotationAssertion( "UBERON:0001009") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "circulatory system") SubClassOf( ) @@ -107114,7 +106215,6 @@ AnnotationAssertion(Annotation( "UBERON:0001016") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -122092,6 +121192,7 @@ AnnotationAssertion(Annotation( "BTO:0001331") "sudoriferous gland") AnnotationAssertion(Annotation( "BTO:0001331") "sudoriparous gland") AnnotationAssertion( "UBERON:0001820") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -125665,6 +124766,7 @@ AnnotationAssertion(Annotation( "BTO:0005132") "erectores pilorum") AnnotationAssertion(Annotation( "BTO:0005132") "pilomotor muscle") AnnotationAssertion( "UBERON:0002033") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arrector muscle of hair") @@ -125944,6 +125046,7 @@ SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -126436,6 +125539,7 @@ AnnotationAssertion( "shaft of hair") AnnotationAssertion(Annotation( "BTO:0004672") "scapus pili") AnnotationAssertion( "UBERON:0002074") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hair shaft") SubClassOf( ) @@ -126480,6 +125584,7 @@ AnnotationAssertion( "MA:0000157") AnnotationAssertion( "hair cuticle") AnnotationAssertion( "UBERON:0002076") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cuticle of hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -126501,6 +125606,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "cortex of coat/hair") AnnotationAssertion( "hair cortex") AnnotationAssertion( "UBERON:0002077") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cortex of hair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -129970,31 +129076,6 @@ DisjointClasses( ) DisjointClasses( ) -# Class: (dorsal mesentery) - -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_mesentery") Annotation( "Wikipedia:Mesentery#Development") Annotation( "ZFIN:curator") "The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA].") -AnnotationAssertion( "EHDAA2:0004560") -AnnotationAssertion( "EHDAA:3019") -AnnotationAssertion( "EHDAA:3033") -AnnotationAssertion( "EHDAA:3921") -AnnotationAssertion( "EHDAA:3934") -AnnotationAssertion( "EHDAA:3957") -AnnotationAssertion( "EHDAA:3971") -AnnotationAssertion( "FMA:79795") -AnnotationAssertion( "SCTID:308823000") -AnnotationAssertion( "TAO:0005130") -AnnotationAssertion( "Wikipedia:Mesentery#Development") -AnnotationAssertion( "ZFA:0005130") -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_mesentery") "dorsal mesogastrium") -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_mesentery") Annotation( ) "mesenterium dorsale commune") -AnnotationAssertion( "UBERON:0002296") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "dorsal mesentery") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (brainstem) AnnotationAssertion(Annotation( "ISBN:0471888893") Annotation( "MP:0005277") Annotation( "Wikipedia:Brainstem") Annotation( "ZFA:0001707") "Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].") @@ -130333,7 +129414,6 @@ AnnotationAssertion( "RETIRED_EHDAA2:0003186") AnnotationAssertion( "SCTID:361348008") AnnotationAssertion( "TAO:0001438") -AnnotationAssertion( "ZFA:0001438") AnnotationAssertion( "galen:BodyCavity") AnnotationAssertion(Annotation( "EHDAA2:0000267") "coelomic cavity") AnnotationAssertion(Annotation( "EHDAA2:0000267") "coelomic cavity lumen") @@ -130620,7 +129700,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (corpus callosum) -AnnotationAssertion(Annotation( "BIRNLEX:1087") "White matter structure containing massive numbers of commissural fibers connecting cortical areas in the two cerebral hemispheres.it is subdivided into a genu, a rostrum, a body, and a splenium. (MM).") +AnnotationAssertion(Annotation( "BIRNLEX:1087") "White matter structure containing massive numbers of commissural fibers connecting cortical areas in the two cerebral hemispheres. It is subdivided into a genu, a rostrum, a body, and a splenium. (MM).") AnnotationAssertion( "BAMS:CC") AnnotationAssertion( "BAMS:cc") AnnotationAssertion( "BIRNLEX:1087") @@ -131564,6 +130644,7 @@ AnnotationAssertion( "BTO:0001387") "Mandel") AnnotationAssertion( "UBERON:0002372") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tonsil") @@ -133565,6 +132646,7 @@ AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "lymphatic drainage system") AnnotationAssertion(Annotation( "Wikipedia:Lymphoid_system") Annotation( ) "systema lymphoideum") AnnotationAssertion( "UBERON:0002465") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymphoid system") @@ -134643,7 +133725,7 @@ SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (digit) @@ -138973,6 +138055,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "rectum mucous membrane") AnnotationAssertion(Annotation( "OBOL:automatic") "rectum organ mucosa") AnnotationAssertion( "UBERON:0003346") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of rectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -146249,6 +145332,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (fallopian tube) AnnotationAssertion(Annotation( "MGI:smb") Annotation( "MP:0003574") Annotation( "http://orcid.org/0000-0002-6601-2165") "Initial section of the oviduct through which the ova pass from the ovary to the uterus.") +AnnotationAssertion(Annotation( "https://sourceforge.net/p/geneontology/ontology-requests/8397/") "mammalian oviduct") AnnotationAssertion(Annotation( ) "salpinges") AnnotationAssertion( "salpinx") AnnotationAssertion( "CALOHA:TS-0732") @@ -146263,9 +145347,8 @@ AnnotationAssertion( "SCTID:181463001") AnnotationAssertion( "Wikipedia:Fallopian_tube") AnnotationAssertion( "galen:FallopianTube") -AnnotationAssertion(Annotation( "https://sourceforge.net/p/geneontology/ontology-requests/8397/") "mammalian oviduct") AnnotationAssertion( "uterine tube (sensu Mammalia)") -AnnotationAssertion( "fallopian tubes") +AnnotationAssertion(Annotation( ) "fallopian tubes") AnnotationAssertion(Annotation( "EHDAA2:0000504") "female paramesonephric duct") AnnotationAssertion(Annotation( "EMAPA:35660") "paramesonephric duct of female") AnnotationAssertion(Annotation( "Wikipedia:Fallopian_tube") Annotation( ) "tuba uterina") @@ -149844,6 +148927,7 @@ AnnotationAssertion( "SCTID:244180007") AnnotationAssertion(Annotation( "OBOL:automatic") "hind limb middle limb segment skin") AnnotationAssertion(Annotation( "OBOL:automatic") "hind limb zeugopod skin") +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-0819-0473") "hindlimb zeugopod skin") AnnotationAssertion( "UBERON:0004264") AnnotationAssertion(rdfs:label "lower leg skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -151335,7 +150419,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch artery") SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -153711,7 +152794,6 @@ AnnotationAssertion( "SCTID:362030008") AnnotationAssertion( "VHOG:0000273") AnnotationAssertion( "UBERON:0004572") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arterial system") SubClassOf( ) @@ -153755,7 +152837,6 @@ AnnotationAssertion( "VHOG:0000277") AnnotationAssertion( "vein system") AnnotationAssertion( "UBERON:0004582") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "venous system") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -154614,7 +153695,6 @@ AnnotationAssertion( "UBERON:0004707") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngula stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -157517,6 +156597,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "mucous membrane of descending colon") AnnotationAssertion(Annotation( "OBOL:automatic") "organ mucosa of descending colon") AnnotationAssertion( "UBERON:0004992") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of descending colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -157534,6 +156615,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "sigmoid colon mucous membrane") AnnotationAssertion(Annotation( "OBOL:automatic") "sigmoid colon organ mucosa") AnnotationAssertion( "UBERON:0004993") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of sigmoid colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -159316,6 +158398,7 @@ AnnotationAssertion( "Wikipedia:Bone_marrow_of_ovary_(hair)") AnnotationAssertion(Annotation( "BTO:0004671") "medulla of hair shaft") AnnotationAssertion( "UBERON:0005184") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hair medulla") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -162612,23 +161695,6 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (dorsal mesogastrium) - -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_mesentery") "The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum.") -AnnotationAssertion( "EHDAA2:0000416") -AnnotationAssertion( "EHDAA:3001") -AnnotationAssertion( "EMAPA:17025") -AnnotationAssertion( "MA:0001618") -AnnotationAssertion( "NCIT:C34142") -AnnotationAssertion( "VHOG:0000352") -AnnotationAssertion( "Wikipedia:Dorsal_mesentery") -AnnotationAssertion(Annotation( "Wikipedia:Dorsal_mesentery") "dorsal mesentery") -AnnotationAssertion( "UBERON:0005602") -AnnotationAssertion(rdfs:label "dorsal mesogastrium") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (extrahepatic part of hepatic duct) AnnotationAssertion( "EMAPA:16844") @@ -163240,20 +162306,6 @@ SubClassOf( ) SubClassOf( ) -# Class: (midgut dorsal mesentery) - -AnnotationAssertion(Annotation( "OBOL:automatic") "A dorsal mesentery that is part of a midgut.") -AnnotationAssertion( "EMAPA:16722") -AnnotationAssertion( "EMAPA:17040") -AnnotationAssertion( "EMAPA:18671") -AnnotationAssertion( "RETIRED_EHDAA2:0001187") -AnnotationAssertion( "SCTID:361434009") -AnnotationAssertion( "UBERON:0005685") -AnnotationAssertion(rdfs:label "midgut dorsal mesentery") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (orbitosphenoid cartilage element) AnnotationAssertion(Annotation( "OBOL:automatic") "An orbitosphenoid endochondral element that is composed primarily of cartilage tissue.") @@ -166661,11 +165713,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "spleen primordium") SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (stapes pre-cartilage condensation) @@ -167181,6 +166230,7 @@ AnnotationAssertion( "MA:0000369") "renal calyx") AnnotationAssertion(Annotation( ) "calices renales") AnnotationAssertion( "UBERON:0006517") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney calyx") SubClassOf( ) @@ -167418,6 +166468,7 @@ AnnotationAssertion(Annotation( "VHOG:0001761") "lymporeticular system") AnnotationAssertion( "UBERON:0006558") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymphatic part of lymphoid system") SubClassOf( ) @@ -170617,7 +169668,6 @@ AnnotationAssertion(Annotation( "BTO:0000449") "embryo late stage") AnnotationAssertion( "UBERON:0007220") AnnotationAssertion(rdfs:label "late embryonic stage") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -172776,6 +171826,7 @@ AnnotationAssertion( "NCIT:C12418") AnnotationAssertion( "SCTID:361355005") AnnotationAssertion( "WikipediaCategory:Head_and_neck") +AnnotationAssertion( "ZFA:0001114") AnnotationAssertion( "galen:HeadAndNeck") AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/379") "cephalic area") AnnotationAssertion(Annotation( "Wikipedia:Head") "cephalic part of animal") @@ -174819,7 +173870,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary acinus") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -175941,7 +174991,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch mesenchymal region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -179864,7 +178914,6 @@ AnnotationAssertion(Annotation( "UBERON:0010341") AnnotationAssertion(rdfs:label "1st arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -179882,7 +178931,6 @@ AnnotationAssertion( "2nd arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -179899,7 +178947,6 @@ AnnotationAssertion( "3rd arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -179916,7 +178963,6 @@ AnnotationAssertion( "4th arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -179930,7 +178976,6 @@ AnnotationAssertion( "UBERON:0010347") AnnotationAssertion(rdfs:label "6th arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -182969,7 +182014,6 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (vertebra pre-cartilage condensation) @@ -182981,7 +182025,7 @@ AnnotationAssertion( "vertebra pre-cartilage condensation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lacrimal nerve) @@ -186001,6 +185045,7 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "UBERON:cjm") Annotation( "Wikipedia:Body_cavity") Annotation( "Wikipedia:Coelom") "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.") AnnotationAssertion( "EHDAA2:0004731") AnnotationAssertion( "Wikipedia:Coelom") +AnnotationAssertion( "ZFA:0001438") AnnotationAssertion(Annotation( "NCBITaxon:33511") "enterocoelom") AnnotationAssertion( "haemocoelom") AnnotationAssertion( "schizocoelom") @@ -193330,6 +192375,7 @@ AnnotationAssertion( "MA:0003087") AnnotationAssertion( "NCIT:C116164") AnnotationAssertion(Annotation( "FMA:37322") "axillary skin") +AnnotationAssertion(Annotation( "PMID:38565739") "skin of armpit") AnnotationAssertion(Annotation( "FMA:37322") "skin of axilla") AnnotationAssertion( "UBERON:0015474") AnnotationAssertion(rdfs:label "axilla skin") @@ -201923,7 +200969,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "UBERON:7500102") AnnotationAssertion(rdfs:label "preorbital bone region") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -202477,6 +201522,17 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (embryonic craniocervical region) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6095-8718") "A craniocervical region that is part of an embryo.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-09-12T14:40:00Z"^^xsd:dateTime) +AnnotationAssertion( "UBERON:8450003") +AnnotationAssertion(rdfs:label "embryonic craniocervical region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (placental blood) AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-6595-0902") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK53254/") "Blood located in the placenta.") @@ -203364,11 +202420,6 @@ SubClassOf( ObjectSomeValuesFrom( )) -EquivalentClasses(ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectExactCardinality(2 ))) -EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectExactCardinality(1 ))) -EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectMinCardinality(2 ))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ) @@ -203376,6 +202427,7 @@ SubClassOf(ObjectIntersectionOf( Obje SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +SubClassOf(ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectSomeValuesFrom( ) ) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) From a37340c7880619be10045e661f83ae4cc10ded74 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Wed, 11 Dec 2024 16:28:42 +0200 Subject: [PATCH 3/3] Removing double space from hp-edit to pass tests --- src/ontology/hp-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/hp-edit.owl b/src/ontology/hp-edit.owl index 049ec0dbe..3fd786e62 100644 --- a/src/ontology/hp-edit.owl +++ b/src/ontology/hp-edit.owl @@ -78970,7 +78970,7 @@ AnnotationAssertion( "Pyramidal signs") AnnotationAssertion( "Pyramidal tract signs") AnnotationAssertion( "HP:0007256") -AnnotationAssertion(rdfs:comment "pyramidal signs are a subset of long-tract signs that specifically indicate corticospinal tract involvement. The more general term long-tract sign refers to a clinical findings related to damage to the long white matter tracts of the CNS, particularly the corticospinal tract, dorsal columns, and the spinothalamic tract.") +AnnotationAssertion(rdfs:comment "pyramidal signs are a subset of long-tract signs that specifically indicate corticospinal tract involvement. The more general term long-tract sign refers to a clinical findings related to damage to the long white matter tracts of the CNS, particularly the corticospinal tract, dorsal columns, and the spinothalamic tract.") AnnotationAssertion(rdfs:label "Abnormal pyramidal sign") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( )