From c70ad16c36d78043f316a16fcd287c340112827f Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Fri, 9 Aug 2024 11:54:07 -0700 Subject: [PATCH 1/4] Adding qudt QuantityKind mappings. See #101 --- .../pato-to-qudt-quantitykind.sssom.tsv | 57 + src/ontology/imports/merged_import.owl | 4002 ++++++----------- 2 files changed, 1462 insertions(+), 2597 deletions(-) create mode 100644 src/mappings/pato-to-qudt-quantitykind.sssom.tsv diff --git a/src/mappings/pato-to-qudt-quantitykind.sssom.tsv b/src/mappings/pato-to-qudt-quantitykind.sssom.tsv new file mode 100644 index 0000000..50f3411 --- /dev/null +++ b/src/mappings/pato-to-qudt-quantitykind.sssom.tsv @@ -0,0 +1,57 @@ +#curie_map: +# PATO: http://purl.obolibrary.org/obo/PATO_ +# oio: http://www.geneontology.org/formats/oboInOwl# +# owl: http://www.w3.org/2002/07/owl# +# quantitykind: http://w3id.org/sssom/unknown_prefix/quantitykind/ +# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# +# rdfs: http://www.w3.org/2000/01/rdf-schema# +# semapv: https://w3id.org/semapv/vocab/ +# skos: http://www.w3.org/2004/02/skos/core# +# sssom: https://w3id.org/sssom/ +# ORCID: "https://orcid.org/" +#creator_id: +# - "ORCID:0000-0002-6601-2165" +#license: https://w3id.org/sssom/license/unspecified +#mapping_set_id: http://purl.obolibrary.org/obo/pato/mappings/pato-to-qudt-quantitykind.sssom.tsv +#mapping_set_description: "Mappings between PATO and qudt QuantityKind types. Seeded using lexmatch then curated" +#license: "https://creativecommons.org/licenses/by/4.0/" +#subject_source: "obo:pato.owl" +#object_source: "quantitykind:" +#mapping_date: "2024-08-09" +subject_id subject_label predicate_id object_id object_label mapping_justification mapping_tool confidence subject_match_field object_match_field match_string +PATO:0000008 speed skos:exactMatch quantitykind:Speed Speed semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label speed +PATO:0000033 concentration of skos:exactMatch quantitykind:Concentration Concentration semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label concentration +PATO:0000057 occurrence skos:exactMatch quantitykind:Incidence Incidence semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label incidence +PATO:0000133 orientation skos:exactMatch quantitykind:Angle Angle semapv:ManualMappingCuration oaklib 1.0 oio:hasRelatedSynonym rdfs:label angle +PATO:0000146 temperature skos:exactMatch quantitykind:Temperature Temperature semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label temperature +PATO:0000915 thickness skos:exactMatch quantitykind:Thickness Thickness semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label thickness +PATO:0000918 volume skos:exactMatch quantitykind:Volume Volume semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label volume +PATO:0000921 width skos:exactMatch quantitykind:Width Width semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label width +PATO:0000970 permeability skos:exactMatch quantitykind:Permeability Permeability semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label permeability +PATO:0000992 viscosity skos:exactMatch quantitykind:Viscosity Viscosity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label viscosity +PATO:0001019 mass density skos:exactMatch quantitykind:Density Density semapv:ManualMappingCuration oaklib 1.0 oio:hasRelatedSynonym rdfs:label density +PATO:0001022 impulse skos:exactMatch quantitykind:Impulse impulse semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label impulse +PATO:0001030 flux skos:exactMatch quantitykind:Flux Flux semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label flux +PATO:0001034 strain skos:exactMatch quantitykind:Strain Strain semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label strain +PATO:0001046 resistance to skos:exactMatch quantitykind:Resistance Resistance semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label resistance +PATO:0001297 reflectivity skos:exactMatch quantitykind:Reflectivity Reflectivity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label reflectivity +PATO:0001309 duration skos:exactMatch quantitykind:Period Period semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label period +PATO:0001352 linear density skos:exactMatch quantitykind:LinearDensity Linear Density semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label linear density +PATO:0001414 catalytic activity skos:exactMatch quantitykind:CatalyticActivity Catalytic Activity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label catalytic activity +PATO:0001470 ratio skos:exactMatch quantitykind:Ratio ratio semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label ratio +PATO:0001521 sound amplitude skos:exactMatch quantitykind:Loudness loudness semapv:ManualMappingCuration oaklib 1.0 oio:hasBroadSynonym rdfs:label loudness +PATO:0001585 conductivity skos:exactMatch quantitykind:Conductivity Conductivity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label conductivity +PATO:0001591 curvature skos:exactMatch quantitykind:Curvature Curvature semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label curvature +PATO:0001595 depth skos:exactMatch quantitykind:Depth Depth semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label depth +PATO:0001679 specific volume skos:exactMatch quantitykind:SpecificVolume Specific Volume semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label specific volume +PATO:0001718 luminance skos:exactMatch quantitykind:Luminance Luminance semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label luminance +PATO:0001740 activity (of a radionuclide) skos:exactMatch quantitykind:Radioactivity radioactivity semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label radioactivity +PATO:0001842 acidity skos:exactMatch quantitykind:Acidity Acidity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label acidity +PATO:0002205 capacitance skos:exactMatch quantitykind:Capacitance Capacitance semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label capacitance +PATO:0002243 fluid flow rate skos:exactMatch quantitykind:VolumeFlowRate Volume Flow Rate semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label volume flow rate +PATO:0002244 mass flow rate skos:exactMatch quantitykind:MassFlowRate Mass Flow Rate semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label mass flow rate +PATO:0002284 tension skos:exactMatch quantitykind:Tension Tension semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label tension +PATO:0002326 angle skos:exactMatch quantitykind:Angle Angle semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label angle +PATO:0002390 radius skos:exactMatch quantitykind:Radius Radius semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label radius + + diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 60eb6f0..29edf71 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,21 +7,19 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-03-28") + +Annotation(owl:versionInfo "2024-05-18") 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()) @@ -53,7 +51,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -67,7 +64,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -99,10 +95,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -116,7 +108,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -147,8 +138,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -157,11 +146,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -194,10 +179,12 @@ 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()) @@ -233,7 +220,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -247,8 +233,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -278,9 +262,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -327,8 +309,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -349,6 +331,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -382,14 +369,12 @@ 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()) @@ -801,7 +786,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -827,6 +811,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1065,8 +1050,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1132,15 +1115,9 @@ 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()) @@ -1149,8 +1126,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1356,8 +1331,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1432,7 +1405,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1539,8 +1511,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1549,26 +1519,21 @@ 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()) @@ -1706,7 +1671,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1752,8 +1716,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1812,7 +1774,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1826,7 +1787,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1857,7 +1817,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1870,7 +1829,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1934,11 +1892,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1965,7 +1920,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1996,7 +1950,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2067,9 +2020,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2111,8 +2061,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2158,7 +2106,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2178,13 +2125,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2280,8 +2224,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2300,8 +2242,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2316,7 +2256,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2512,7 +2451,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2544,11 +2482,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2614,10 +2550,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2647,9 +2579,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2746,13 +2675,8 @@ 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()) @@ -2806,7 +2730,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3011,7 +2934,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3035,7 +2957,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3134,7 +3055,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3184,8 +3104,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3199,8 +3117,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3230,7 +3146,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3243,7 +3158,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3393,10 +3307,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3413,12 +3323,11 @@ 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()) @@ -3586,7 +3495,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3716,9 +3624,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3806,7 +3711,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3940,7 +3844,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3972,9 +3875,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4222,6 +4122,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4350,7 +4251,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6032,14 +5933,10 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6047,16 +5944,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6112,8 +6000,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6129,12 +6015,8 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6163,30 +6045,13 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6204,20 +6069,14 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6229,25 +6088,17 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6256,9 +6107,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6314,7 +6162,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6360,19 +6207,21 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6426,7 +6275,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6475,9 +6323,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) -Declaration(AnnotationProperty(rdfs:seeAlso)) Declaration(AnnotationProperty(owl:deprecated)) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6492,7 +6338,7 @@ Declaration(AnnotationProperty()) AnnotationAssertion(rdfs:label "definition") -# Annotation Property: (preferred_root) +# Annotation Property: (has ontology root term) AnnotationAssertion( "IAO:0000700") AnnotationAssertion( "external") @@ -6501,7 +6347,6 @@ AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "has_ontology_root_term") AnnotationAssertion(rdfs:label "has ontology root term") -AnnotationAssertion(rdfs:label "preferred_root") # Annotation Property: (term replaced by) @@ -6612,10 +6457,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -6632,6 +6473,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -6656,6 +6501,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -6664,6 +6513,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -6868,12 +6721,6 @@ AnnotationAssertion(rdfs:label "shorthand") -# Annotation Property: rdfs:seeAlso (see also) - -AnnotationAssertion( rdfs:seeAlso "http://www.w3.org/2000/01/rdf-schema#seeAlso") -AnnotationAssertion( rdfs:seeAlso "seeAlso") -AnnotationAssertion(rdfs:label rdfs:seeAlso "see also") - ############################ # Object Properties @@ -7111,19 +6958,6 @@ AnnotationAssertion(rdfs:label "has ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (function of) - -AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) -AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) -AnnotationAssertion( "function_of"@en) -AnnotationAssertion( "is function of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "function of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - # Object Property: (quality of) AnnotationAssertion( "this red color is a quality of this apple"@en) @@ -7148,17 +6982,6 @@ AnnotationAssertion(rdfs:label "role SubObjectPropertyOf( ) InverseObjectProperties( ) -# Object Property: (has function) - -AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) -AnnotationAssertion( "has_function"@en) -AnnotationAssertion(rdfs:label "has function"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - # Object Property: (has quality) AnnotationAssertion( "this apple has quality this red color"@en) @@ -7180,23 +7003,6 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (has disposition) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has disposition"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (disposition of) - -AnnotationAssertion( "inverse of has disposition") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "disposition of"@en) -SubObjectPropertyOf( ) - # Object Property: (location of) AnnotationAssertion( "is location of"@en) @@ -7302,61 +7108,6 @@ SubObjectPropertyOf( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ) -# Object Property: (has regulatory component activity) - -AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002013") -AnnotationAssertion( "external") -AnnotationAssertion( "has_regulatory_component_activity") -AnnotationAssertion( "has_regulatory_component_activity") -AnnotationAssertion(rdfs:label "has regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has negative regulatory component activity) - -AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) -AnnotationAssertion( "RO:0002014") -AnnotationAssertion( "external") -AnnotationAssertion( "has_negative_regulatory_component_activity") -AnnotationAssertion( "has_negative_regulatory_component_activity") -AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") -AnnotationAssertion(rdfs:label "has negative regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has positive regulatory component activity) - -AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") -AnnotationAssertion(rdfs:label "has positive regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has component activity) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") -AnnotationAssertion(rdfs:label "has component activity") -SubObjectPropertyOf( ) - -# Object Property: (has component process) - -AnnotationAssertion( "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has component process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - # Object Property: (occurs across) AnnotationAssertion( "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.") @@ -7365,43 +7116,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "occurs across") SubObjectPropertyOf( ) -# Object Property: (directly regulated by) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") -AnnotationAssertion(rdfs:label "directly regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly negatively regulated by) - -AnnotationAssertion(Annotation( ) "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly negatively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly positively regulated by) - -AnnotationAssertion(Annotation( ) "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly positively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has effector activity) - -AnnotationAssertion(Annotation( ) "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") -AnnotationAssertion(rdfs:label "has effector activity") -SubObjectPropertyOf( ) -FunctionalObjectProperty() - # Object Property: (before or simultaneous with) AnnotationAssertion( "David Osumi-Sutherland") @@ -8198,25 +7912,6 @@ InverseObjectProperties( ) ObjectPropertyRange( ) -# Object Property: (acts upstream of) - -AnnotationAssertion( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") -AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within) - -AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") -AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") -AnnotationAssertion( "affects") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) -SubObjectPropertyOf( ) - # Object Property: (developmentally replaces) AnnotationAssertion( ) @@ -8425,23 +8120,6 @@ AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development") AnnotationAssertion(rdfs:label "developmentally related to"@en) -# Object Property: (enables) - -AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") -AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") -AnnotationAssertion( ) -AnnotationAssertion( "catalyzes") -AnnotationAssertion( "executes") -AnnotationAssertion( "has") -AnnotationAssertion( "is catalyzing") -AnnotationAssertion( "is executing") -AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enables"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - # Object Property: (functionally related to) AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") @@ -8457,44 +8135,6 @@ AnnotationAssertion( "part of structure that is capable of"@en) SubObjectPropertyOf( ) -# Object Property: (involved in) - -AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") -AnnotationAssertion( ) -AnnotationAssertion( "actively involved in") -AnnotationAssertion( "enables part of") -AnnotationAssertion(rdfs:label "involved in"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (regulates levels of) - -AnnotationAssertion( "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid") -AnnotationAssertion( "p regulates levels of c if p regulates some amount (PATO:0000070) of c") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "regulates levels of (process to entity)") -AnnotationAssertion( "RO:0002332") -AnnotationAssertion( "external") -AnnotationAssertion( "regulates_levels_of") -AnnotationAssertion( "regulates_levels_of") -AnnotationAssertion(rdfs:label "regulates levels of"@en) -AnnotationAssertion(rdfs:label "regulates levels of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (enabled by) - -AnnotationAssertion( "inverse of enables") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enabled by"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (regulated by) AnnotationAssertion( "inverse of regulates") @@ -8647,7 +8287,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has member"@en) SubObjectPropertyOf( ) -IrreflexiveObjectProperty() # Object Property: (input of) @@ -8828,44 +8467,6 @@ SubObjectPropertyOf( ) InverseObjectProperties( ) -# Object Property: (immediately causally downstream of) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002405") -AnnotationAssertion( "external") -AnnotationAssertion( "immediately_causally_downstream_of") -AnnotationAssertion( "immediately_causally_downstream_of") -AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) -AnnotationAssertion(rdfs:label "immediately causally downstream of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (indirectly positively regulates) - -AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly activates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (indirectly negatively regulates) - -AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly inhibits") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - # Object Property: (causally related to) AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") @@ -8904,20 +8505,6 @@ SubObjectPropertyOf( ) TransitiveObjectProperty() -# Object Property: (immediately causally upstream of) - -AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002412") -AnnotationAssertion( "external") -AnnotationAssertion( "immediately_causally_upstream_of") -AnnotationAssertion( "immediately_causally_upstream_of") -AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) -AnnotationAssertion(rdfs:label "immediately causally upstream of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (causally upstream of or within) AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") @@ -8948,54 +8535,6 @@ AnnotationAssertion(rdfs:label "caus SubObjectPropertyOf( ) TransitiveObjectProperty() -# Object Property: (involved in regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (involved in positive regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in positive regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in negative regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in negative regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in or involved in regulation of) - -AnnotationAssertion( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") -AnnotationAssertion( "OWL does not allow defining object properties via a Union") -AnnotationAssertion( ) -AnnotationAssertion( "involved in or reguates") -AnnotationAssertion(rdfs:label "involved in or involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (is active in) - -AnnotationAssertion( "A protein that enables activity in a cytosol.") -AnnotationAssertion(Annotation( ) Annotation( ) "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") -AnnotationAssertion( ) -AnnotationAssertion( "executes activity in") -AnnotationAssertion( "enables activity in") -AnnotationAssertion(rdfs:comment "") -AnnotationAssertion(rdfs:label "is active in") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Is_active_in"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (contributes to morphology of) AnnotationAssertion( "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.") @@ -9003,88 +8542,6 @@ AnnotationAssertion( "contributes to morphology of") SubObjectPropertyOf( ) -# Object Property: (interacts with) - -AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) -AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") -AnnotationAssertion( ) -AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") -AnnotationAssertion( "in pairwise interaction with") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interacts with") -AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) -SymmetricObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (molecularly interacts with) - -AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") -AnnotationAssertion( ) -AnnotationAssertion( "binds") -AnnotationAssertion( "molecularly binds with") -AnnotationAssertion(rdfs:label "molecularly interacts with") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) -SubObjectPropertyOf( ) -SymmetricObjectProperty() - -# Object Property: (phosphorylates) - -AnnotationAssertion( "Axiomatization to GO to be added later") -AnnotationAssertion( ) -AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") -AnnotationAssertion(rdfs:label "phosphorylates") -SubObjectPropertyOf( ) - -# Object Property: (directly regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "molecularly controls") -AnnotationAssertion(rdfs:label "directly regulates activity of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly negatively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly inhibits") -AnnotationAssertion( "molecularly decreases activity of") -AnnotationAssertion(rdfs:label "directly negatively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly positively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly activates") -AnnotationAssertion( "molecularly increases activity of") -AnnotationAssertion(rdfs:label "directly positively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (helper property (not for use in curation)) - -AnnotationAssertion( ) -AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") -AnnotationAssertion(rdfs:label "helper property (not for use in curation)") - # Object Property: (composed primarily of) AnnotationAssertion( "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'") @@ -9107,12 +8564,6 @@ AnnotationAssertion(rdfs:label "has ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (is kinase activity) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "is kinase activity") -SubObjectPropertyOf( ) - # Object Property: (receives input from) AnnotationAssertion( "See notes for inverse relation") @@ -9253,17 +8704,6 @@ AnnotationAssertion( "towards") SubObjectPropertyOf( ) -# Object Property: (causal relation between entities) - -AnnotationAssertion( "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causal relation between entities") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - # Object Property: (has skeleton) AnnotationAssertion( "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'") @@ -9275,33 +8715,9 @@ AnnotationAssertion(rdfs:label "has SubObjectPropertyOf( ) InverseObjectProperties( ) AsymmetricObjectProperty() -IrreflexiveObjectProperty() ObjectPropertyDomain( ) ObjectPropertyRange(Annotation( "This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.") ) -# Object Property: (causally influenced by) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influenced by (entity-centric)") -AnnotationAssertion(rdfs:label "causally influenced by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (interaction relation helper property) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interaction relation helper property") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (molecular interaction relation helper property) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "molecular interaction relation helper property") -SubObjectPropertyOf( ) - # Object Property: (results in movement of) AnnotationAssertion( "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c") @@ -9317,18 +8733,6 @@ AnnotationAssertion( "results in movement of") SubObjectPropertyOf( ) -# Object Property: (causally influences) - -AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influences (entity-centric)") -AnnotationAssertion(rdfs:label "causally influences") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - # Object Property: (biomechanically related to) AnnotationAssertion( "A relation that holds between elements of a musculoskeletal system or its analogs.") @@ -9391,24 +8795,6 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (directly regulates) - -AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly regulates (processual)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002578") -AnnotationAssertion( "external") -AnnotationAssertion( "directly_regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly_regulates") -AnnotationAssertion(rdfs:label "directly regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (has part structure that is capable of) AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") @@ -9509,42 +8895,6 @@ AnnotationAssertion( "Groups both positive and negative correlation") AnnotationAssertion(rdfs:label "correlated with") -# Object Property: (directly positively regulates) - -AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly positively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002629") -AnnotationAssertion( "external") -AnnotationAssertion( "directly_positively_regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly_positively_regulates") -AnnotationAssertion(rdfs:label "directly positively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (directly negatively regulates) - -AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly negatively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002630") -AnnotationAssertion( "external") -AnnotationAssertion( "directly_negatively_regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly_negatively_regulates") -AnnotationAssertion(rdfs:label "directly negatively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (produces) AnnotationAssertion( ) @@ -9618,57 +8968,15 @@ AnnotationAssertion(rdfs:label "has SubObjectPropertyOf( ) SubObjectPropertyOf( ) -# Object Property: (enables subfunction) - -AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "enables subfunction") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, positive effect) - -AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, negative effect) - -AnnotationAssertion( "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) +# Object Property: (realized in response to stimulus) + +AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-12-26T19:45:49Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "realized in response to stimulus") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) # Object Property: (causally upstream of or within, negative effect) @@ -9688,14 +8996,22 @@ AnnotationAssertion(rdfs:label "caus AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) -# Object Property: (regulates activity of) - -AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +# Object Property: (realized in response to) + +AnnotationAssertion( "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.") +AnnotationAssertion( "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") +AnnotationAssertion( "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.") +AnnotationAssertion( "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "triggered by process") +AnnotationAssertion(rdfs:label "realized in response to"@en) +AnnotationAssertion(rdfs:seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) # Object Property: (acts on population of) @@ -9728,23 +9044,6 @@ AnnotationAssertion(rdfs:label "resu AnnotationAssertion(rdfs:label "results in fusion of") SubObjectPropertyOf( ) -# Object Property: (indirectly causally upstream of) - -AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) -SubObjectPropertyOf( ) - -# Object Property: (indirectly regulates) - -AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (different in magnitude relative to) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") @@ -9795,49 +9094,14 @@ AnnotationAssertion(rdfs:label "reci AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) -# Object Property: (regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0019000") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "regulates_characteristic") -AnnotationAssertion( "regulates_characteristic") -AnnotationAssertion(rdfs:label "regulates characteristic") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (positively regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0019001") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "positively_regulates_characteristic") -AnnotationAssertion( "positively_regulates_characteristic") -AnnotationAssertion(rdfs:label "positively regulates characteristic") -SubObjectPropertyOf( ) - -# Object Property: (negatively regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0019002") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "negatively_regulates_characteristic") -AnnotationAssertion( "negatively_regulates_characteristic") -AnnotationAssertion(rdfs:label "negatively regulates characteristic") -SubObjectPropertyOf( ) - # Object Property: (results in changes to anatomical or cellular structure) AnnotationAssertion( "p has anatomical participant c iff p has participant c, and c is an anatomical entity") @@ -9972,93 +9236,20 @@ AnnotationAssertion(rdfs:seeAlso (continuant) +# Class: () -AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) -AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (occurrent) +# Class: () -AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) -AnnotationAssertion(rdfs:label "occurrent"@en) -SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (independent continuant) - -AnnotationAssertion( "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) -AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) -AnnotationAssertion(rdfs:label "independent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (spatial region) - -AnnotationAssertion(rdfs:label "spatial region"@en) -SubClassOf( ) - -# Class: (process) - -AnnotationAssertion( "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) -AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) -AnnotationAssertion(rdfs:label "process"@en) -SubClassOf( ) - -# Class: (disposition) - -AnnotationAssertion(rdfs:label "disposition"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (realizable entity) - -AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) -AnnotationAssertion(rdfs:label "realizable entity"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (quality) - -AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (specifically dependent continuant) - -AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) -AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) -AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (role) - -AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) -AnnotationAssertion(rdfs:label "role"@en) -SubClassOf( ) - -# Class: (function) - -AnnotationAssertion(rdfs:label "function"@en) -SubClassOf( ) +# Class: () -# Class: (material entity) - -AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) -AnnotationAssertion(rdfs:label "material entity"@en) -SubClassOf( ) -DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (immaterial entity) +# Class: () -AnnotationAssertion(rdfs:label "immaterial entity"@en) -SubClassOf( ) DisjointClasses( ObjectSomeValuesFrom( )) # Class: (electron) @@ -10998,43 +10189,6 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (phosphate(3-)) - -AnnotationAssertion( "A phosphate ion that is the conjugate base of hydrogenphosphate.") -AnnotationAssertion( "-3") -AnnotationAssertion( "O4P") -AnnotationAssertion( "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3") -AnnotationAssertion( "NBIIXXVUZAFLBC-UHFFFAOYSA-K") -AnnotationAssertion( "94.97136") -AnnotationAssertion( "94.95507") -AnnotationAssertion( "[O-]P([O-])([O-])=O") -AnnotationAssertion( "CHEBI:14791") -AnnotationAssertion( "CHEBI:45024") -AnnotationAssertion( "CHEBI:7793") -AnnotationAssertion(Annotation( "Beilstein") "Beilstein:3903772") -AnnotationAssertion(Annotation( "ChemIDplus") "CAS:14265-44-2") -AnnotationAssertion(Annotation( "KEGG COMPOUND") "CAS:14265-44-2") -AnnotationAssertion(Annotation( "Gmelin") "Gmelin:1997") -AnnotationAssertion( "KEGG:C00009") -AnnotationAssertion(Annotation( "ChEBI") "PDBeChem:PO4") -AnnotationAssertion(Annotation( "Reaxys") "Reaxys:3903772") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "phosphate") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "tetraoxidophosphate(3-)") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "tetraoxophosphate(3-)") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "tetraoxophosphate(V)") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Orthophosphate") -AnnotationAssertion(Annotation( "PDBeChem") "PHOSPHATE ION") -AnnotationAssertion(Annotation( "IUPAC") "PO4(3-)") -AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Phosphate") -AnnotationAssertion(Annotation( "IUPAC") "[PO4](3-)") -AnnotationAssertion( "CHEBI:18367") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphate(3-)") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (acyl group) AnnotationAssertion( "An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.") @@ -11227,16 +10381,6 @@ AnnotationAssertion( "drug") SubClassOf( ) -# Class: (monoatomic cation) - -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "monoatomic cations") -AnnotationAssertion( "CHEBI:23906") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "monoatomic cation") -SubClassOf( ) -SubClassOf( ) - # Class: (enzyme inhibitor) AnnotationAssertion( "A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.") @@ -11643,93 +10787,6 @@ AnnotationAssertion(rdfs:label "pep SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (phosphate) - -AnnotationAssertion( "Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "phosphates") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "phosphates") -AnnotationAssertion( "CHEBI:26020") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphate") -SubClassOf( ) - -# Class: (phosphoric acid) - -AnnotationAssertion( "A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom.") -AnnotationAssertion( "0") -AnnotationAssertion( "H3O4P") -AnnotationAssertion( "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)") -AnnotationAssertion( "NBIIXXVUZAFLBC-UHFFFAOYSA-N") -AnnotationAssertion( "97.99520") -AnnotationAssertion( "97.97690") -AnnotationAssertion( "[H]OP(=O)(O[H])O[H]") -AnnotationAssertion(Annotation( "Beilstein") "Beilstein:1921286") -AnnotationAssertion(Annotation( "ChemIDplus") "CAS:7664-38-2") -AnnotationAssertion(Annotation( "KEGG COMPOUND") "CAS:7664-38-2") -AnnotationAssertion(Annotation( "NIST Chemistry WebBook") "CAS:7664-38-2") -AnnotationAssertion(Annotation( "DrugCentral") "Drug_Central:4478") -AnnotationAssertion(Annotation( "Gmelin") "Gmelin:2000") -AnnotationAssertion( "HMDB:HMDB0002142") -AnnotationAssertion( "KEGG:C00009") -AnnotationAssertion( "KEGG:D05467") -AnnotationAssertion( "KNApSAcK:C00007408") -AnnotationAssertion(Annotation( "Europe PMC") "PMID:11455380") -AnnotationAssertion(Annotation( "Europe PMC") "PMID:15630224") -AnnotationAssertion(Annotation( "Europe PMC") "PMID:17439666") -AnnotationAssertion(Annotation( "Europe PMC") "PMID:17518491") -AnnotationAssertion(Annotation( "Europe PMC") "PMID:22282755") -AnnotationAssertion(Annotation( "Europe PMC") "PMID:22333268") -AnnotationAssertion(Annotation( "Europe PMC") "PMID:22381614") -AnnotationAssertion(Annotation( "Europe PMC") "PMID:22401268") -AnnotationAssertion(Annotation( "Reaxys") "Reaxys:1921286") -AnnotationAssertion( "Wikipedia:Phosphoric_Acid") -AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Phosphoric acid") -AnnotationAssertion(Annotation( "IUPAC") "phosphoric acid") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "tetraoxophosphoric acid") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "trihydrogen tetraoxophosphate(3-)") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "trihydroxidooxidophosphorus") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "IUPAC") "H3PO4") -AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Orthophosphoric acid") -AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Phosphate") -AnnotationAssertion(Annotation( "ChEBI") "Phosphorsaeure") -AnnotationAssertion(Annotation( "ChEBI") "Phosphorsaeureloesungen") -AnnotationAssertion(Annotation( "IUPAC") "[PO(OH)3]") -AnnotationAssertion(Annotation( "ChEBI") "acide phosphorique") -AnnotationAssertion(Annotation( "ChEBI") "acidum phosphoricum") -AnnotationAssertion(Annotation( "NIST_Chemistry_WebBook") "orthophosphoric acid") -AnnotationAssertion( "CHEBI:26078") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphoric acid") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (phosphoric acid derivative) - -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:26079") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphoric acid derivative") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (phosphorus molecular entity) - -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "phosphorus molecular entities") -AnnotationAssertion( "CHEBI:26082") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphorus molecular entity") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (steroid hormone) AnnotationAssertion( "Any steroid that acts as hormone.") @@ -12009,39 +11066,6 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (phosphorus atom) - -AnnotationAssertion( "0") -AnnotationAssertion( "P") -AnnotationAssertion( "InChI=1S/P") -AnnotationAssertion( "OAICVXFJPJFONN-UHFFFAOYSA-N") -AnnotationAssertion( "30.97376") -AnnotationAssertion( "30.97376") -AnnotationAssertion( "[P]") -AnnotationAssertion( "CHEBI:26080") -AnnotationAssertion( "CHEBI:8168") -AnnotationAssertion(Annotation( "ChemIDplus") "CAS:7723-14-0") -AnnotationAssertion(Annotation( "KEGG COMPOUND") "CAS:7723-14-0") -AnnotationAssertion(Annotation( "Gmelin") "Gmelin:16235") -AnnotationAssertion( "KEGG:C06262") -AnnotationAssertion( "WebElements:P") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "phosphorus") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "IUPAC") "15P") -AnnotationAssertion(Annotation( "IUPAC") "P") -AnnotationAssertion(Annotation( "KEGG_COMPOUND") "P") -AnnotationAssertion(Annotation( "ChEBI") "Phosphor") -AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Phosphorus") -AnnotationAssertion(Annotation( "ChEBI") "fosforo") -AnnotationAssertion(Annotation( "ChEBI") "phosphore") -AnnotationAssertion(Annotation( "ChEBI") "phosphorus") -AnnotationAssertion( "CHEBI:28659") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphorus atom") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (serotonin) AnnotationAssertion( "A primary amino compound that is the 5-hydroxy derivative of tryptamine.") @@ -12417,7 +11441,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic group") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (organyl group) @@ -12599,31 +11624,6 @@ AnnotationAssertion( "heteroorganic entity") SubClassOf( ) -# Class: (agrochemical) - -AnnotationAssertion( "An agrochemical is a substance that is used in agriculture or horticulture.") -AnnotationAssertion( "Wikipedia:Agrochemical") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "agrichemical") -AnnotationAssertion(Annotation( "ChEBI") "agrichemicals") -AnnotationAssertion(Annotation( "ChEBI") "agricultural chemicals") -AnnotationAssertion(Annotation( "ChEBI") "agrochemicals") -AnnotationAssertion( "CHEBI:33286") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "agrochemical") -SubClassOf( ) - -# Class: (fertilizer) - -AnnotationAssertion( "A fertilizer is any substance that is added to soil or water to assist the growth of plants.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "fertiliser") -AnnotationAssertion(Annotation( "ChEBI") "fertilizers") -AnnotationAssertion( "CHEBI:33287") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "fertilizer") -SubClassOf( ) - # Class: (pnictogen) AnnotationAssertion( "Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.") @@ -12750,17 +11750,6 @@ AnnotationAssertion(rdfs:label "sul SubClassOf( ) SubClassOf( ) -# Class: (pnictogen oxoacid) - -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "pnictogen oxoacids") -AnnotationAssertion( "CHEBI:33408") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "pnictogen oxoacid") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (sulfur oxoacid derivative) AnnotationAssertion(Annotation( "ChEBI") "sulfur oxoacid derivative") @@ -12772,44 +11761,6 @@ AnnotationAssertion(rdfs:label "sul SubClassOf( ) SubClassOf( ) -# Class: (phosphorus oxoacid) - -AnnotationAssertion( "A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons.") -AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoacid") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "Oxosaeure des Phosphors") -AnnotationAssertion(Annotation( "ChEBI") "oxoacids of phosphorus") -AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoacids") -AnnotationAssertion( "CHEBI:33457") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphorus oxoacid") -SubClassOf( ) -SubClassOf( ) - -# Class: (pnictogen oxoanion) - -AnnotationAssertion(Annotation( "ChEBI") "pnictogen oxoanion") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "pnictogen oxoanions") -AnnotationAssertion( "CHEBI:33459") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "pnictogen oxoanion") -SubClassOf( ) -SubClassOf( ) - -# Class: (phosphorus oxoanion) - -AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoanion") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "oxoanions of phosphorus") -AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoanions") -AnnotationAssertion( "CHEBI:33461") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphorus oxoanion") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - # Class: (sulfur oxoanion) AnnotationAssertion(Annotation( "ChEBI") "sulfur oxoanion") @@ -12983,7 +11934,7 @@ SubClassOf( ObjectSomeValuesFrom( "A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.") AnnotationAssertion( "0") AnnotationAssertion( "CHO2R") -AnnotationAssertion( "45.01740") +AnnotationAssertion( "45.017") AnnotationAssertion( "44.99765") AnnotationAssertion( "OC([*])=O") AnnotationAssertion( "CHEBI:13428") @@ -13263,6 +12214,19 @@ AnnotationAssertion(rdfs:label "pol SubClassOf( ) SubClassOf( ) +# Class: (amino-acid cation) + +AnnotationAssertion(Annotation( "ChEBI") "amino-acid cation") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "amino acid cation") +AnnotationAssertion(Annotation( "ChEBI") "amino-acid cations") +AnnotationAssertion( "CHEBI:33703") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "amino-acid cation") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (alpha-amino acid) AnnotationAssertion( "An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.") @@ -13289,6 +12253,7 @@ AnnotationAssertion( "alpha-amino acid") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (amino-acid residue) @@ -13302,6 +12267,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino-acid residue") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (amino acid) @@ -13321,6 +12288,7 @@ AnnotationAssertion(rdfs:label "ami SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (alpha-amino-acid residue) @@ -13339,6 +12307,18 @@ AnnotationAssertion(rdfs:label "alp SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (alpha-amino-acid cation) + +AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid cation") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "alpha-amino acid cations") +AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid cations") +AnnotationAssertion( "CHEBI:33719") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "alpha-amino-acid cation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (carbohydrate acid) AnnotationAssertion(Annotation( "ChEBI") "carbohydrate acid") @@ -13833,20 +12813,6 @@ AnnotationAssertion(rdfs:label "mon SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (phosphate ion) - -AnnotationAssertion( "A phosphorus oxoanion that is the conjugate base of phosphoric acid.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "Pi") -AnnotationAssertion(Annotation( "ChEBI") "phosphate") -AnnotationAssertion(Annotation( "ChEBI") "phosphate ions") -AnnotationAssertion( "CHEBI:35780") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphate ion") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (pnictogen hydride) AnnotationAssertion(Annotation( "ChEBI") "pnictogen hydride") @@ -13989,25 +12955,6 @@ AnnotationAssertion(rdfs:label "pol SubClassOf( ) SubClassOf( ) -# Class: (phosphorus oxoacid derivative) - -AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoacid derivative") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:36359") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphorus oxoacid derivative") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (phosphorus oxoacids and derivatives) - -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:36360") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphorus oxoacids and derivatives") -SubClassOf( ) - # Class: (carbonyl compound) AnnotationAssertion( "Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.") @@ -14400,38 +13347,6 @@ AnnotationAssertion(rdfs:label "Lew SubClassOf( ) SubClassOf( ) -# Class: (dihydrogenphosphate) - -AnnotationAssertion( "A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated.") -AnnotationAssertion( "-1") -AnnotationAssertion( "H2O4P") -AnnotationAssertion( "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-1") -AnnotationAssertion( "NBIIXXVUZAFLBC-UHFFFAOYSA-M") -AnnotationAssertion( "96.98724") -AnnotationAssertion( "96.96962") -AnnotationAssertion( "[H]OP([O-])(=O)O[H]") -AnnotationAssertion( "CHEBI:29137") -AnnotationAssertion( "CHEBI:39739") -AnnotationAssertion( "DrugBank:DB02831") -AnnotationAssertion(Annotation( "Gmelin") "Gmelin:1999") -AnnotationAssertion( "PDBeChem:2HP") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydrogen(tetraoxidophosphate)(1-)") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydrogenphosphate") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydrogentetraoxophosphate(1-)") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydrogentetraoxophosphate(V)") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydroxidodioxidophosphate(1-)") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "PDBeChem") "DIHYDROGENPHOSPHATE ION") -AnnotationAssertion(Annotation( "IUPAC") "H2PO4(-)") -AnnotationAssertion(Annotation( "IUPAC") "[PO2(OH)2](-)") -AnnotationAssertion( "CHEBI:39745") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "dihydrogenphosphate") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (hydroxy group) AnnotationAssertion( "0") @@ -14454,45 +13369,6 @@ AnnotationAssertion( "hydroxy group") SubClassOf( ) -# Class: (hydrogenphosphate) - -AnnotationAssertion( "A phosphate ion that is the conjugate base of dihydrogenphosphate.") -AnnotationAssertion( "-2") -AnnotationAssertion( "HO4P") -AnnotationAssertion( "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-2") -AnnotationAssertion( "NBIIXXVUZAFLBC-UHFFFAOYSA-L") -AnnotationAssertion( "95.97930") -AnnotationAssertion( "95.96234") -AnnotationAssertion( "OP([O-])([O-])=O") -AnnotationAssertion( "CHEBI:29139") -AnnotationAssertion( "CHEBI:43470") -AnnotationAssertion(Annotation( "Gmelin") "Gmelin:1998") -AnnotationAssertion( "MolBase:1628") -AnnotationAssertion( "PDBeChem:PI") -AnnotationAssertion( "PDBeChem:PO4") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydrogen(tetraoxidophosphate)(2-)") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydrogenphosphate") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydrogentetraoxophosphate(2-)") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydrogentetraoxophosphate(V)") -AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydroxidotrioxidophosphate(2-)") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "IUPAC") "HPO4(2-)") -AnnotationAssertion(Annotation( "PDBeChem") "HYDROGENPHOSPHATE ION") -AnnotationAssertion(Annotation( "PDBeChem") "INORGANIC PHOSPHATE GROUP") -AnnotationAssertion(Annotation( "MolBase") "[P(OH)O3](2-)") -AnnotationAssertion(Annotation( "IUPAC") "[PO3(OH)](2-)") -AnnotationAssertion(Annotation( "ChEBI") "hydrogen phosphate") -AnnotationAssertion(Annotation( "UniProt") "phosphate") -AnnotationAssertion( "CHEBI:43474") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "hydrogenphosphate") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (hydrogensulfate) AnnotationAssertion( "-1") @@ -14824,7 +13700,6 @@ AnnotationAssertion( "CHEBI:50906") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "role") -SubClassOf( ) # Class: (neurotoxin) @@ -15121,6 +13996,23 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (cationic amino-acid residue) + +AnnotationAssertion( "An amino-acid residue protonated on nitrogen.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "amino acid cation residue") +AnnotationAssertion(Annotation( "ChEBI") "amino acid cation residues") +AnnotationAssertion(Annotation( "ChEBI") "amino-acid cation residue") +AnnotationAssertion(Annotation( "ChEBI") "amino-acid cation residues") +AnnotationAssertion(Annotation( "ChEBI") "cationic amino acid residue") +AnnotationAssertion(Annotation( "ChEBI") "cationic amino acid residues") +AnnotationAssertion(Annotation( "ChEBI") "cationic amino-acid residues") +AnnotationAssertion( "CHEBI:58942") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cationic amino-acid residue") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (organosulfate oxoanion) AnnotationAssertion( "An organic anion of general formula RS(=O)2O(-) where R is an organyl group.") @@ -15139,15 +14031,6 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (phosphoric acids) - -AnnotationAssertion( "Compounds containing one or more phosphoric acid units.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:59698") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphoric acids") -SubClassOf( ) - # Class: (nucleophilic reagent) AnnotationAssertion( "A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.") @@ -15434,6 +14317,65 @@ AnnotationAssertion( "organic acid") SubClassOf( ) +# Class: (cationic group) + +AnnotationAssertion( "A group that carries an overall positive charge.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "cationic groups") +AnnotationAssertion( "CHEBI:64766") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cationic group") +SubClassOf( ) + +# Class: (anionic group) + +AnnotationAssertion( "A group that carries an overall negative charge.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "anionic groups") +AnnotationAssertion( "CHEBI:64767") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anionic group") +SubClassOf( ) + +# Class: (organic cationic group) + +AnnotationAssertion( "A cationic group that contains carbon.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "organic cationic groups") +AnnotationAssertion( "CHEBI:64769") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "organic cationic group") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organic anionic group) + +AnnotationAssertion( "An anionic group that contains carbon.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "organic anionic groups") +AnnotationAssertion( "CHEBI:64775") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "organic anionic group") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anionic amino-acid residue) + +AnnotationAssertion( "An amino-acid residue carrying an overall negative charge.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "amino acid anion residue") +AnnotationAssertion(Annotation( "ChEBI") "amino acid anion residues") +AnnotationAssertion(Annotation( "ChEBI") "amino-acid anion residue") +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") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (poison) AnnotationAssertion( "Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.") @@ -15912,16 +14854,6 @@ AnnotationAssertion( "carbohydrates and carbohydrate derivatives") SubClassOf( ) -# Class: (trivalent inorganic anion) - -AnnotationAssertion( "Any inorganic anion with a valency of three.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "trivalent inorganic anions") -AnnotationAssertion( "CHEBI:79387") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "trivalent inorganic anion") -SubClassOf( ) - # Class: (divalent inorganic anion) AnnotationAssertion( "Any inorganic anion with a valency of two.") @@ -15983,21 +14915,11 @@ AnnotationAssertion(rdfs:label "hyd SubClassOf( ) SubClassOf( ) -# Class: (algal metabolite) - -AnnotationAssertion( "Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "algal metabolites") -AnnotationAssertion( "CHEBI:84735") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "algal metabolite") -SubClassOf( ) - # Class: (cell) AnnotationAssertion(Annotation( "CARO:mah") "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") AnnotationAssertion( "CALOHA:TS-2035") -AnnotationAssertion( "FBbt:00007002") +AnnotationAssertion(Annotation( ) "FBbt:00007002") AnnotationAssertion( "FMA:68646") AnnotationAssertion( "GO:0005623") AnnotationAssertion( "KUPO:0000002") @@ -16005,6 +14927,7 @@ AnnotationAssertion( "VHOG:0001533") AnnotationAssertion( "WBbt:0004017") AnnotationAssertion( "XAO:0003012") +AnnotationAssertion(Annotation( ) "ZFA:0009000") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).") @@ -16015,48 +14938,57 @@ DisjointClasses( ) DisjointClasses( ) -# Class: (fibroblast neural crest derived) +# Class: (neural crest derived fibroblast) -AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-5208-3432") "Any fibroblast that is deriived from the neural crest.") -AnnotationAssertion(rdfs:label "fibroblast neural crest derived") +AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-5208-3432") "Any fibroblast that is derived from the neural crest.") +AnnotationAssertion( "fibroblast neural crest derived") +AnnotationAssertion(rdfs:label "neural crest derived fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuronal receptor cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.") +AnnotationAssertion(Annotation( ) "ZFA:0009001") AnnotationAssertion( "neuronal receptor cell (sensu Animalia)") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuronal receptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (early embryonic cell (metazoa)) AnnotationAssertion(Annotation( "GOC:tfm") "A cell found in the embryo before the formation of all the gem layers is complete.") +AnnotationAssertion(Annotation( ) "ZFA:0009002") AnnotationAssertion(rdfs:label "early embryonic cell (metazoa)") SubClassOf( ) # Class: (migratory cranial neural crest cell) AnnotationAssertion(Annotation( "ZFA:0007091") Annotation( "https://orcid.org/0000-0001-5208-3432") "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.") +AnnotationAssertion(Annotation( ) "ZFA:0007091") AnnotationAssertion(rdfs:label "migratory cranial neural crest cell") SubClassOf( ) # Class: (migratory trunk neural crest cell) AnnotationAssertion(Annotation( "ZFA:0007095") Annotation( "https://orcid.org/0000-0001-5208-3432") "Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination.") +AnnotationAssertion(Annotation( ) "ZFA:0007095") AnnotationAssertion(rdfs:label "migratory trunk neural crest cell") SubClassOf( ) # Class: (germ line stem cell) AnnotationAssertion(Annotation( "doi:10.1016/j.stem.2012.05.016") "A stem cell that is the precursor of gametes.") -AnnotationAssertion( "FBbt:00004861") +AnnotationAssertion(Annotation( ) "FBbt:00004861") +AnnotationAssertion(Annotation( ) "ZFA:0005956") AnnotationAssertion( "germline stem cell") AnnotationAssertion(rdfs:label "germ line stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) # Class: (female germ cell) @@ -16068,11 +15000,12 @@ AnnotationAssertion( "female germ cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female germ line stem cell) AnnotationAssertion(Annotation( "doi:10.1016/j.stem.2012.05.016") "A stem cell that is the precursor of female gametes.") -AnnotationAssertion( "FBbt:00004873") +AnnotationAssertion(Annotation( ) "FBbt:00004873") AnnotationAssertion(rdfs:label "female germ line stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -16083,14 +15016,17 @@ SubClassOf(Annotation( AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") "A female germ cell that has entered meiosis.") AnnotationAssertion( "BTO:0000964") AnnotationAssertion( "CALOHA:TS-0711") -AnnotationAssertion( "FBbt:00004886") +AnnotationAssertion(Annotation( ) "FBbt:00004886") AnnotationAssertion( "FMA:18644") AnnotationAssertion( "MESH:D009865") AnnotationAssertion( "WBbt:0006797") +AnnotationAssertion(Annotation( ) "ZFA:0001109") AnnotationAssertion( "oogonium") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "oocyte") +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -16098,11 +15034,14 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "ISBN:0721662544") "An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.") AnnotationAssertion( "FMA:83673") +AnnotationAssertion(Annotation( ) "ZFA:0005878") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "oogonial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (egg cell) @@ -16110,13 +15049,15 @@ AnnotationAssertion(Annotation( "BTO:0000369") AnnotationAssertion( "BTO:0003801") AnnotationAssertion( "CALOHA:TS-2191") -AnnotationAssertion( "FBbt:00057012") +AnnotationAssertion(Annotation( ) "FBbt:00057012") AnnotationAssertion( "FMA:67343") AnnotationAssertion( "MESH:D010063") +AnnotationAssertion(Annotation( ) "ZFA:0001570") AnnotationAssertion( "mature oocyte") AnnotationAssertion( "ovum") AnnotationAssertion(rdfs:label "egg cell") AnnotationAssertion( "https://www.swissbiopics.org/api/image/Egg_cell.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -16131,16 +15072,21 @@ SubClassOf( ObjectSomeValuesFrom( (neural crest derived neuron) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any neuron that develops from some migratory neural crest cell.") +AnnotationAssertion(Annotation( ) "ZFA:0009009") AnnotationAssertion( "neuron neural crest derived") AnnotationAssertion(rdfs:label "neural crest derived neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (glioblast) +AnnotationAssertion(Annotation( ) "ZFA:0009010") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "glioblast") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -16149,10 +15095,12 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:NV") Annotation( "http://en.wikipedia.org/wiki/Neuroblast") "A cell that will develop into a neuron often after a migration phase.") AnnotationAssertion( "BTO:0000930") AnnotationAssertion( "FMA:70563") +AnnotationAssertion(Annotation( ) "ZFA:0009011") AnnotationAssertion( "neuroblast") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuroblast (sensu Vertebrata)") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (stem cell) @@ -16161,6 +15109,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "CALOHA:TS-2086") AnnotationAssertion( "FMA:63368") +AnnotationAssertion(Annotation( ) "ZFA:0005957") AnnotationAssertion( "animal stem cell") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16168,18 +15117,21 @@ 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( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (single fate stem cell) AnnotationAssertion(Annotation( "GOC:tfm") "A stem cell that self-renews as well as give rise to a single mature cell type.") AnnotationAssertion( "FMA:70569") +AnnotationAssertion(Annotation( ) "ZFA:0009013") AnnotationAssertion( "unipotent stem cell") AnnotationAssertion( "unipotential stem cell") AnnotationAssertion(rdfs:label "single fate stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hematopoietic stem cell) @@ -16190,6 +15142,7 @@ AnnotationAssertion( "FMA:86475") AnnotationAssertion( "MESH:D006412") AnnotationAssertion( "VHOG:0001485") +AnnotationAssertion(Annotation( ) "ZFA:0009014") AnnotationAssertion( "blood forming stem cell") AnnotationAssertion( "hemopoietic stem cell") AnnotationAssertion(Annotation( ) "HSC") @@ -16200,14 +15153,29 @@ AnnotationAssertion( "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.") AnnotationAssertion(rdfs:label "hematopoietic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (erythroid progenitor cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0721601464") "A progenitor cell committed to the erythroid lineage.") AnnotationAssertion( "BTO:0004911") +AnnotationAssertion(Annotation( ) "ZFA:0009015") AnnotationAssertion(Annotation( ) "BFU-E") AnnotationAssertion(Annotation( ) "CFU-E") AnnotationAssertion( "blast forming unit erythroid") @@ -16224,6 +15192,7 @@ SubClassOf( ObjectSomeValuesFrom( (germ line cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.") +AnnotationAssertion(Annotation( ) "ZFA:0009016") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Originally this term had some plant germ line cell children.") @@ -16235,18 +15204,22 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:add") "A stem cell that can give rise to multiple lineages of cells.") AnnotationAssertion( "FMA:84789") +AnnotationAssertion(Annotation( ) "ZFA:0009020") AnnotationAssertion( "multi-fate stem cell") AnnotationAssertion( "multifate stem cell") AnnotationAssertion( "multipotent cell") AnnotationAssertion( "multipotent stem cell") AnnotationAssertion(rdfs:label "multi fate stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (common myeloid progenitor) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0878932437") Annotation( "MESH:D023461") "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0004730") +AnnotationAssertion(Annotation( ) "ZFA:0009021") AnnotationAssertion( "common myeloid precursor") AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-GEMM") AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-S") @@ -16267,6 +15240,7 @@ DisjointClasses( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "MESH:D055015") Annotation( "PMID:16647566") Annotation( "http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell") "A progenitor cell committed to the megakaryocyte and erythroid lineages.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "ZFA:0009022") AnnotationAssertion( "CFU-EM") AnnotationAssertion( "CFU-MegE") AnnotationAssertion( "MEP") @@ -16279,13 +15253,17 @@ AnnotationAssertion( "MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.") AnnotationAssertion(rdfs:label "megakaryocyte-erythroid progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (common lymphoid progenitor) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "PMID:10407577") Annotation( "PMID:16551251") "A oligopotent progenitor cell committed to the lymphoid lineage.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "ZFA:0009023") AnnotationAssertion( "common lymphocyte precursor") AnnotationAssertion( "common lymphocyte progenitor") AnnotationAssertion( "common lymphoid precursor") @@ -16301,12 +15279,15 @@ AnnotationAssertion(rdfs:comment "CL AnnotationAssertion(rdfs:label "common lymphoid progenitor") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (totipotent stem cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:tfm") "A stem cell from which all cells of the body can form.") AnnotationAssertion( "FMA:84790") AnnotationAssertion( "MESH:D039901") +AnnotationAssertion(Annotation( ) "ZFA:0009024") AnnotationAssertion( "totipotential stem cell") AnnotationAssertion(rdfs:label "totipotent stem cell") SubClassOf( ) @@ -16320,17 +15301,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "define using PATO mulit-potent or oligopotent?") AnnotationAssertion(rdfs:label "non-terminally differentiated cell") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (myoblast) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "MESH:D032446") Annotation( "PMID:21849021") "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.") AnnotationAssertion( "BTO:0000222") AnnotationAssertion( "CALOHA:TS-0650") -AnnotationAssertion( "FBbt:00005083") +AnnotationAssertion(Annotation( ) "FBbt:00005083") AnnotationAssertion( "FMA:70335") AnnotationAssertion( "VHOG:0001529") +AnnotationAssertion(Annotation( ) "ZFA:0009025") AnnotationAssertion(rdfs:label "myoblast") SubClassOf( ) @@ -16343,11 +15324,13 @@ AnnotationAssertion( "FMA:63877") AnnotationAssertion( "NCIT:C12482") AnnotationAssertion( "VHOG:0001482") +AnnotationAssertion(Annotation( ) "ZFA:0009026") AnnotationAssertion( ) AnnotationAssertion( ) 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( )) @@ -16356,8 +15339,10 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "GO_REF:0000034") Annotation( "ISBN:0618947256") "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell.") AnnotationAssertion( "BTO:0003607") AnnotationAssertion( "FMA:66783") +AnnotationAssertion(Annotation( ) "ZFA:0009027") AnnotationAssertion( "chrondoplast") AnnotationAssertion(rdfs:label "chondroblast") +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -16368,9 +15353,12 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "A cell that has a filiform extrusion of the cell surface.") AnnotationAssertion( "VHOG:0001532") AnnotationAssertion( "XAO:0000031") +AnnotationAssertion(Annotation( ) "ZFA:0009032") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ciliated cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell) @@ -16379,9 +15367,10 @@ AnnotationAssertion( "BTO:0000414") AnnotationAssertion( "CALOHA:TS-2026") AnnotationAssertion( "CARO:0000077") -AnnotationAssertion( "FBbt:00000124") +AnnotationAssertion(Annotation( ) "FBbt:00000124") AnnotationAssertion( "FMA:66768") AnnotationAssertion( "WBbt:0003672") +AnnotationAssertion(Annotation( ) "ZFA:0009034") AnnotationAssertion( "epitheliocyte") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16396,22 +15385,28 @@ DisjointClasses( "GOC:tfm") "An epithelial cell that has a cilia.") AnnotationAssertion( "FMA:70605") +AnnotationAssertion(Annotation( ) "ZFA:0009035") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ciliated epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (duct epithelial cell) AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-5208-3432") "An epithelial cell that is part of a duct.") +AnnotationAssertion(Annotation( ) "ZFA:0009372") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duct epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vessel endothelial cell) AnnotationAssertion(Annotation( "GOC:tfm") "An endothelial cell that lines the vasculature.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "ZFA:0009036") AnnotationAssertion( "cuboidal endothelial cell of vascular tree") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16419,12 +15414,14 @@ AnnotationAssertion(rdfs:label "bloo EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (columnar/cuboidal epithelial cell) AnnotationAssertion(Annotation( "GO:0002065") Annotation( "https://orcid.org/0000-0001-5208-3432") "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "ZFA:0009038") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "columnar/cuboidal epithelial cell") @@ -16433,6 +15430,7 @@ SubClassOf( (squamous epithelial cell) AnnotationAssertion( "CALOHA:TS-1249") +AnnotationAssertion(Annotation( ) "ZFA:0009039") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "squamous epithelial cell") SubClassOf( ) @@ -16442,30 +15440,36 @@ SubClassOf( "GOC:tfm") Annotation( "ISBN:0721662544") "A flattened epithelial cell of mesenchymal origin that lines the serous cavity.") AnnotationAssertion( ) AnnotationAssertion( "FMA:66773") +AnnotationAssertion(Annotation( ) "ZFA:0009040") AnnotationAssertion( "mesotheliocyte") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell") SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (circulating cell) AnnotationAssertion(Annotation( "GOC:add") "A cell which moves among different tissues of the body, via blood, lymph, or other medium.") +AnnotationAssertion(Annotation( ) "ZFA:0009043") AnnotationAssertion(rdfs:label "circulating cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:tfm") "A cell found predominately in the blood.") AnnotationAssertion( "FMA:62844") AnnotationAssertion( "MESH:D001773") +AnnotationAssertion(Annotation( ) "ZFA:0009044") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of lung) @@ -16475,12 +15479,14 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuron associated cell) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuron associated cell") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -16489,9 +15495,11 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "ISBN:0517223651") Annotation( "ISBN:0721662544") "A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells.") AnnotationAssertion( "neuroepithelial cell") AnnotationAssertion( "BTO:0004301") +AnnotationAssertion(Annotation( ) "ZFA:0009050") AnnotationAssertion(rdfs:comment "The term \"neuroepithelial cell\" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710).") AnnotationAssertion(rdfs:label "sensory epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (interneuron) @@ -16499,9 +15507,10 @@ SubClassOf( "GOC:tfm") Annotation( "MESH:D007395") "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0003811") -AnnotationAssertion( "FBbt:00005125") +AnnotationAssertion(Annotation( ) "FBbt:00005125") AnnotationAssertion( "FMA:67313") AnnotationAssertion( "WBbt:0005113") +AnnotationAssertion(Annotation( ) "ZFA:0009051") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interneuron") @@ -16512,9 +15521,10 @@ SubClassOf( "MESH:D009046") Annotation( "PMID:16875686") "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0000312") -AnnotationAssertion( "FBbt:00005123") +AnnotationAssertion(Annotation( ) "FBbt:00005123") AnnotationAssertion( "FMA:83617") AnnotationAssertion( "WBbt:0005409") +AnnotationAssertion(Annotation( ) "ZFA:0009052") AnnotationAssertion( "motoneuron") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16524,50 +15534,66 @@ SubClassOf( (sensory neuron) AnnotationAssertion(Annotation( "ISBN:0721662544") "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.") +AnnotationAssertion( ) AnnotationAssertion( "BTO:0001037") -AnnotationAssertion( "FBbt:00005124") +AnnotationAssertion(Annotation( ) "FBbt:00005124") AnnotationAssertion( "FMA:84649") AnnotationAssertion( "MESH:D011984") AnnotationAssertion( "WBbt:0005759") +AnnotationAssertion(Annotation( ) "ZFA:0009053") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sensory neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bipolar neuron) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0444009442") "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.") AnnotationAssertion( "FMA:67282") +AnnotationAssertion(Annotation( ) "ZFA:0009055") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bipolar neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (multipolar neuron) AnnotationAssertion(Annotation( "FMA:67287") Annotation( "GOC:tfm") "A neuron with three or more neurites, usually an axon and multiple dendrites.") AnnotationAssertion( "FMA:67287") +AnnotationAssertion(Annotation( ) "ZFA:0009056") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "multipolar neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (autonomic neuron) AnnotationAssertion(Annotation( "GOC:tfm") "A neuron whose cell body is within an autonomic ganglion.") AnnotationAssertion( "FMA:80121") +AnnotationAssertion(Annotation( ) "ZFA:0009059") AnnotationAssertion(rdfs:label "autonomic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cholinergic neuron) AnnotationAssertion(Annotation( "GOC:tfm") "A neuron that uses acetylcholine as a vesicular neurotransmitter.") AnnotationAssertion( "BTO:0004902") -AnnotationAssertion( "FBbt:00007173") +AnnotationAssertion(Annotation( ) "FBbt:00007173") AnnotationAssertion( "FMA:84796") AnnotationAssertion( "MESH:D059329") AnnotationAssertion( "WBbt:0006840") +AnnotationAssertion(Annotation( ) "ZFA:0009060") AnnotationAssertion(rdfs:label "cholinergic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell) @@ -16576,6 +15602,7 @@ AnnotationAssertion( "BTO:0001176") AnnotationAssertion( "CALOHA:TS-0278") AnnotationAssertion( "FMA:66772") +AnnotationAssertion(Annotation( ) "ZFA:0009065") AnnotationAssertion( "endotheliocyte") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16586,7 +15613,9 @@ SubClassOf( (CNS neuron (sensu Vertebrata)) +AnnotationAssertion(Annotation( ) "ZFA:0009067") AnnotationAssertion(rdfs:label "CNS neuron (sensu Vertebrata)") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -16595,30 +15624,38 @@ SubClassOf( ObjectSomeValuesFrom( "ISBN:9780123973481") "A neuron that has dendritic processes radiating from the cell body forming a star-like shape.") AnnotationAssertion( "BTO:0002316") +AnnotationAssertion(Annotation( ) "ZFA:0009072") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stellate neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuron associated cell (sensu Vertebrata)) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuron associated cell (sensu Vertebrata)") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (glial cell) AnnotationAssertion(Annotation( "MESH:D009457") "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.") +AnnotationAssertion( ) AnnotationAssertion( "BTO:0002606") AnnotationAssertion( "CALOHA:TS-0415") -AnnotationAssertion( "FBbt:00005144") +AnnotationAssertion(Annotation( ) "FBbt:00005144") AnnotationAssertion( "FMA:54536") +AnnotationAssertion(Annotation( ) "ZFA:0009073") AnnotationAssertion( "neuroglial cell") AnnotationAssertion( "neuroglia") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571") AnnotationAssertion(rdfs:label "glial cell") SubClassOf( ) @@ -16629,6 +15666,7 @@ AnnotationAssertion(Annotation( "BTO:0000771") AnnotationAssertion( "CALOHA:TS-2027") AnnotationAssertion( "FMA:54538") +AnnotationAssertion(Annotation( ) "ZFA:0009074") AnnotationAssertion( "macrogliocyte") AnnotationAssertion(Annotation( "doi:10.1152/physrev.2001.81.2.871") Annotation( ) "macroglia") AnnotationAssertion( ) @@ -16643,6 +15681,7 @@ AnnotationAssertion( "BTO:0000962") AnnotationAssertion( "CALOHA:TS-0709") AnnotationAssertion( "FMA:54540") +AnnotationAssertion(Annotation( ) "ZFA:0009076") AnnotationAssertion(Annotation( "PMID:8734446") "OLs") AnnotationAssertion( "oligodendroglia") AnnotationAssertion( ) @@ -16650,13 +15689,14 @@ AnnotationAssertion( "Oligodendrocytes are reportedly MDP-positive and CD4-negative.") AnnotationAssertion(rdfs:label "oligodendrocyte") SubClassOf(Annotation( "true") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neurectodermal cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:068340007X") "Ectoderm destined to be nervous tissue.") +AnnotationAssertion(Annotation( ) "ZFA:0009080") AnnotationAssertion( "neurectoderm cell") AnnotationAssertion(rdfs:label "neurectodermal cell") SubClassOf( ) @@ -16667,6 +15707,7 @@ AnnotationAssertion(Annotation( "BTO:0002625") AnnotationAssertion( "BTO:0003298") AnnotationAssertion( "FMA:70546") +AnnotationAssertion(Annotation( ) "ZFA:0009081") AnnotationAssertion( "bone marrow stromal cells") AnnotationAssertion( "colony-forming unit-fibroblast") AnnotationAssertion(Annotation( "PMID:11378515") "marrow stromal cells") @@ -16693,12 +15734,14 @@ AnnotationAssertion( "BTO:0000443") AnnotationAssertion( "CALOHA:TS-0012") AnnotationAssertion( "FMA:63880") +AnnotationAssertion(Annotation( ) "ZFA:0009082") AnnotationAssertion( "adipose cell") AnnotationAssertion( "fat cell") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "adipocyte") +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -16709,12 +15752,12 @@ AnnotationAssertion(Annotation( "BTO:0000249") AnnotationAssertion( "CALOHA:TS-0138") AnnotationAssertion( "FMA:66782") +AnnotationAssertion(Annotation( ) "ZFA:0009084") AnnotationAssertion( "cartilage cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chondrocyte") SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -16722,6 +15765,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "A pigment cell is a cell that contains pigment granules.") AnnotationAssertion( "VHOG:0001678") +AnnotationAssertion(Annotation( ) "ZFA:0009090") AnnotationAssertion( "chromatocyte") AnnotationAssertion( "chromatophore") AnnotationAssertion(rdfs:label "pigment cell") @@ -16752,19 +15796,24 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "secretory cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (exocrine cell) AnnotationAssertion(Annotation( "ISBN:0198547684") "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.") AnnotationAssertion( "FMA:16014") +AnnotationAssertion(Annotation( ) "ZFA:0009092") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "exocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glycosaminoglycan secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") "A cell that secretes glycosaminoglycans.") +AnnotationAssertion(Annotation( ) "ZFA:0009093") AnnotationAssertion( "GAG secreting cell") AnnotationAssertion( "hyaluronic acid secreting cell") AnnotationAssertion(rdfs:label "glycosaminoglycan secreting cell") @@ -16773,8 +15822,11 @@ SubClassOf( (protein secreting cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is capable of some protein secretion.") AnnotationAssertion(rdfs:label "protein secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (seromucus secreting cell) @@ -16786,13 +15838,16 @@ SubClassOf( "MESH:D055098") "A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.") AnnotationAssertion( ) AnnotationAssertion( "FMA:83809") +AnnotationAssertion(Annotation( ) "ZFA:0009096") AnnotationAssertion( "endocrinocyte") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (enteroendocrine cell) @@ -16800,6 +15855,7 @@ AnnotationAssertion(Annotation( "BTO:0003865") AnnotationAssertion( "FMA:62930") AnnotationAssertion( "MESH:D019858") +AnnotationAssertion(Annotation( ) "ZFA:0009097") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enteroendocrine cell") SubClassOf( ) @@ -16810,8 +15866,9 @@ SubClassOf( "MESH:D055099") "A neuron that is capable of some hormone secretion in response to neuronal signals.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0002691") -AnnotationAssertion( "FBbt:00005130") +AnnotationAssertion(Annotation( ) "FBbt:00005130") AnnotationAssertion( "FMA:83810") +AnnotationAssertion(Annotation( ) "ZFA:0009098") AnnotationAssertion( "neurosecretory cell") AnnotationAssertion( "neurosecretory neuron") AnnotationAssertion( ) @@ -16822,32 +15879,46 @@ The modern definition of neurosecretion has evolved to include the release of an AnnotationAssertion(rdfs:label "neuroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) # Class: (peptide hormone secreting cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is capable of some peptide hormone secretion.") +AnnotationAssertion(Annotation( ) "ZFA:0009100") AnnotationAssertion(rdfs:label "peptide hormone secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glucagon secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") "A cell that secretes glucagon.") AnnotationAssertion( "FMA:84045") +AnnotationAssertion(Annotation( ) "ZFA:0009103") AnnotationAssertion( "glucagon-secreting cell") AnnotationAssertion(rdfs:label "glucagon secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatostatin secreting cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is capable of some somatostatin secretion.") +AnnotationAssertion(Annotation( ) "ZFA:0009105") AnnotationAssertion(rdfs:label "somatostatin secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (steroid hormone secreting cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is capable of some steroid hormone secretion.") +AnnotationAssertion(Annotation( ) "ZFA:0009106") AnnotationAssertion(rdfs:label "steroid hormone secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (contractile cell) @@ -16862,14 +15933,16 @@ AnnotationAssertion(Annotation( "BTO:0000888") AnnotationAssertion( "BTO:0000902") AnnotationAssertion( "CALOHA:TS-2032") -AnnotationAssertion( "FBbt:00005074") +AnnotationAssertion(Annotation( ) "FBbt:00005074") AnnotationAssertion( "FMA:67328") AnnotationAssertion( "WBbt:0003675") +AnnotationAssertion(Annotation( ) "ZFA:0009114") AnnotationAssertion( "muscle fiber") AnnotationAssertion( "myocyte") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle cell") AnnotationAssertion( "https://www.swissbiopics.org/api/image/Muscle_cells.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -16881,12 +15954,15 @@ AnnotationAssertion( "BTO:0004392") AnnotationAssertion( "CALOHA:TS-2158") AnnotationAssertion( "FMA:9727") +AnnotationAssertion(Annotation( ) "ZFA:0009115") AnnotationAssertion( "skeletal muscle cell") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell of skeletal muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell) @@ -16896,6 +15972,7 @@ AnnotationAssertion( "BTO:0004576") AnnotationAssertion( "CALOHA:TS-2159") AnnotationAssertion( "FMA:14072") +AnnotationAssertion(Annotation( ) "ZFA:0009118") AnnotationAssertion(Annotation( "PMID:9315361") "SMCs") AnnotationAssertion(Annotation( "MESH:D032389") "myocytes, smooth muscle") AnnotationAssertion( "smooth muscle fiber") @@ -16914,45 +15991,59 @@ AnnotationAssertion( "receptor cell") AnnotationAssertion(rdfs:label "sensory receptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (chemoreceptor cell) AnnotationAssertion(Annotation( "MESH:D002628") "A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood.") +AnnotationAssertion(Annotation( ) "ZFA:0009124") AnnotationAssertion(rdfs:label "chemoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (taste receptor cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0618947256") "A specialized cell involved in gustatory sensory perception.") AnnotationAssertion( "FMA:67910") +AnnotationAssertion(Annotation( ) "ZFA:0009126") AnnotationAssertion( "taste bud cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "taste receptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (photoreceptor cell) AnnotationAssertion(Annotation( "MESH:D010786") "A cell specialized to detect and transduce light.") AnnotationAssertion( "BTO:0001060") AnnotationAssertion( "CALOHA:TS-0868") +AnnotationAssertion(Annotation( ) "FBbt:00004211") AnnotationAssertion( "FMA:86740") +AnnotationAssertion(Annotation( ) "ZFA:0009127") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "photoreceptor cell") AnnotationAssertion( "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (electrically active cell) AnnotationAssertion(Annotation( "FB:ma") "A cell whose function is determined by the generation or the reception of an electric signal.") +AnnotationAssertion(Annotation( ) "ZFA:0009128") AnnotationAssertion(rdfs:label "electrically active cell") SubClassOf( ) # Class: (lining cell) AnnotationAssertion(Annotation( "JB:jb") "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.") +AnnotationAssertion(Annotation( ) "ZFA:0009130") AnnotationAssertion( "boundary cell") AnnotationAssertion(rdfs:label "lining cell") SubClassOf( ) @@ -16961,6 +16052,7 @@ SubClassOf( "A cell located in the synovial joint.") AnnotationAssertion( "CALOHA:TS-0995") +AnnotationAssertion(Annotation( ) "ZFA:0009131") AnnotationAssertion( "synoviocyte") AnnotationAssertion(rdfs:label "synovial cell") SubClassOf( ) @@ -16970,11 +16062,13 @@ SubClassOf( ObjectSomeValuesFrom( (barrier cell) AnnotationAssertion(Annotation( "JB:jb") "A cell whose primary function is to prevent the transport of stuff across compartments.") +AnnotationAssertion(Annotation( ) "ZFA:0009132") AnnotationAssertion(rdfs:label "barrier cell") SubClassOf( ) # Class: (insulating cell) +AnnotationAssertion(Annotation( ) "ZFA:0009134") AnnotationAssertion(rdfs:label "insulating cell") SubClassOf( ) @@ -16985,23 +16079,28 @@ AnnotationAssertion( "peripheral neuroglial cell") AnnotationAssertion( "CALOHA:TS-0898") AnnotationAssertion( "FMA:62121") +AnnotationAssertion(Annotation( ) "ZFA:0009135") AnnotationAssertion( "neurilemmal cell") AnnotationAssertion(rdfs:label "myelinating Schwann cell") SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (motile cell) AnnotationAssertion(Annotation( "FB:ma") "A cell that moves by its own activities.") +AnnotationAssertion(Annotation( ) "ZFA:0009136") AnnotationAssertion(rdfs:label "motile cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ectodermal cell) AnnotationAssertion(Annotation( "MESH:D004475") "A cell of the outer of the three germ layers of the embryo.") AnnotationAssertion( "FMA:72549") +AnnotationAssertion(Annotation( ) "ZFA:0009137") AnnotationAssertion( "ectoderm cell") AnnotationAssertion(rdfs:label "ectodermal cell") SubClassOf( ) @@ -17011,6 +16110,7 @@ SubClassOf( ObjectSomeValuesFrom( "MESH:D008648") "A cell of the middle germ layer of the embryo.") AnnotationAssertion( "FMA:72554") +AnnotationAssertion(Annotation( ) "ZFA:0009138") AnnotationAssertion( "mesoblast") AnnotationAssertion( "mesoderm cell") AnnotationAssertion( ) @@ -17022,6 +16122,7 @@ SubClassOf( ObjectSomeValuesFrom( "MESH:D004707") "A cell of the inner of the three germ layers of the embryo.") AnnotationAssertion( "FMA:72555") +AnnotationAssertion(Annotation( ) "ZFA:0009139") AnnotationAssertion( "endoderm cell") AnnotationAssertion(rdfs:label "endodermal cell") SubClassOf( ) @@ -17034,6 +16135,8 @@ AnnotationAssertion( "non-nucleated cell") AnnotationAssertion(rdfs:label "anucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (single nucleate cell) @@ -17041,11 +16144,16 @@ DisjointClasses( "FB:ma") Annotation( "GOC:tfm") "A cell with a single nucleus.") AnnotationAssertion(rdfs:label "single nucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +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) @@ -17057,6 +16165,8 @@ AnnotationAssertion( "syncytium") AnnotationAssertion(rdfs:label "multinucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (erythrocyte) @@ -17072,35 +16182,49 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (eukaryotic cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that only exists in Eukaryota.") AnnotationAssertion( "MESH:D005057") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eukaryotic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Eumycetozoan cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that only exists in Eumycetozoa.") AnnotationAssertion(rdfs:label "Eumycetozoan cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (eye photoreceptor cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any photoreceptor cell that is part of some eye.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "ZFA:0009154") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eye photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (structural cell) AnnotationAssertion(Annotation( "TAIR:sr") "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.") +AnnotationAssertion(Annotation( ) "ZFA:0005745") AnnotationAssertion(rdfs:label "structural cell") SubClassOf( ) @@ -17108,13 +16232,16 @@ SubClassOf( "GOC:tfm") Annotation( "ISBN:0721662544") "A mature sexual reproductive cell having a single set of unpaired chromosomes.") AnnotationAssertion( "CALOHA:TS-0395") -AnnotationAssertion( "FBbt:00005412") +AnnotationAssertion(Annotation( ) "FBbt:00005412") AnnotationAssertion( "FMA:18649") +AnnotationAssertion(Annotation( ) "ZFA:0009156") AnnotationAssertion( "haploid nucleated cell") AnnotationAssertion( "haploid germ cell") AnnotationAssertion(rdfs:label "gamete") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (crystallin accumulating cell) @@ -17142,27 +16269,34 @@ SubClassOf( (extracellular matrix secreting cell) +AnnotationAssertion(Annotation( ) "ZFA:0009162") AnnotationAssertion(rdfs:label "extracellular matrix secreting cell") SubClassOf( ) # Class: (oxygen accumulating cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that is capable of some oxygen transport.") +AnnotationAssertion(Annotation( ) "ZFA:0009164") AnnotationAssertion(rdfs:label "oxygen accumulating cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (migratory neural crest cell) AnnotationAssertion(Annotation( "doi:10.1016/j.stem.2015.02.017") "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.") AnnotationAssertion( "FMA:86667") +AnnotationAssertion(Annotation( ) "ZFA:0007086") AnnotationAssertion(rdfs:label "migratory neural crest cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme condensation cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:5025404") "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.") +AnnotationAssertion(Annotation( ) "ZFA:0009166") AnnotationAssertion(rdfs:label "mesenchyme condensation cell") SubClassOf( ) @@ -17170,33 +16304,46 @@ SubClassOf( "GOC:tfm") Annotation( "ISBN:0618947256") "An early neural cell developing from the early ependymal cell of the neural tube.") AnnotationAssertion( "FMA:70564") +AnnotationAssertion(Annotation( ) "ZFA:0009169") AnnotationAssertion( "spongioblast") AnnotationAssertion(rdfs:label "glioblast (sensu Vertebrata)") SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (scleral cell) AnnotationAssertion(Annotation( "GOC:add") "A cell of the sclera of the eye.") +AnnotationAssertion(Annotation( ) "ZFA:0009174") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "scleral cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (choroidal cell of the eye) AnnotationAssertion(Annotation( "GOC:add") "A structural cell that is part of optic choroid.") +AnnotationAssertion(Annotation( ) "ZFA:0009175") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "choroidal cell of the eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (extraembryonic cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that is part of some extraembryonic structure.") +AnnotationAssertion(Annotation( ) "ZFA:0009176") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "extraembryonic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trophoblast cell) @@ -17218,6 +16365,7 @@ SubClassOf( "MESH:D001756") "An undifferentiated cell produced by early cleavages of the fertilized egg (zygote).") AnnotationAssertion( "BTO:0001473") AnnotationAssertion( "FMA:72551") +AnnotationAssertion(Annotation( ) "ZFA:0009177") AnnotationAssertion( "blastomere") AnnotationAssertion(rdfs:label "blastoderm cell") SubClassOf( ) @@ -17226,15 +16374,18 @@ SubClassOf( "PMID:18282570") "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell.") AnnotationAssertion( "FMA:86767") +AnnotationAssertion(Annotation( ) "ZFA:0009179") AnnotationAssertion(rdfs:comment "Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo.") AnnotationAssertion(rdfs:label "multi-potent skeletal muscle stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) # Class: (vascular associated smooth muscle cell) AnnotationAssertion(Annotation( "GOC:dsd") Annotation( "GOC:tfm") "A smooth muscle cell associated with the vasculature.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "ZFA:0009181") AnnotationAssertion( "VSMC") AnnotationAssertion( "vascular smooth muscle cell") AnnotationAssertion( ) @@ -17243,6 +16394,7 @@ AnnotationAssertion(rdfs:label "vasc EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epidermal cell) @@ -17251,12 +16403,14 @@ AnnotationAssertion( "CALOHA:TS-0283") AnnotationAssertion( "FMA:62411") AnnotationAssertion( "MESH:D000078404") +AnnotationAssertion(Annotation( ) "ZFA:0009183") AnnotationAssertion(Annotation( "FMA:62411") "cell of epidermis") AnnotationAssertion(Annotation( "FMA:62411") "epithelial cell of skin") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epidermal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (animal zygote) @@ -17268,33 +16422,42 @@ AnnotationAssertion( "animal zygote") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (electrically responsive cell) AnnotationAssertion(Annotation( "FB:ma") "A cell whose function is determined by its response to an electric signal.") +AnnotationAssertion(Annotation( ) "ZFA:0009190") AnnotationAssertion(rdfs:label "electrically responsive cell") SubClassOf( ) # Class: (ganglion interneuron) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any interneuron that has its soma located in some ganglion.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ganglion interneuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (CNS interneuron) AnnotationAssertion(Annotation( "doi:10.1016/B978-0-12-817424-1.00001-X") "An interneuron that has its cell body in a central nervous system.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "ZFA:0009191") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system.") AnnotationAssertion(rdfs:label "CNS interneuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (electrically signaling cell) AnnotationAssertion(Annotation( "FB:ma") "A cell that initiates an electrical signal and passes that signal to another cell.") +AnnotationAssertion(Annotation( ) "ZFA:0009193") AnnotationAssertion(rdfs:label "electrically signaling cell") SubClassOf( ) @@ -17303,12 +16466,16 @@ SubClassOf( "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) Annotation( "FB:ma") Annotation( "PMID:32646579") "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label "polyploid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (haploid cell) AnnotationAssertion(Annotation( "FB:ma") Annotation( "GOC:tfm") "A cell whose nucleus contains a single haploid genome.") AnnotationAssertion(rdfs:label "haploid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (obliquely striated muscle cell) @@ -17316,6 +16483,8 @@ AnnotationAssertion(Annotation( "Examples include the somatic muscles of nemotodes and cephalopods.") AnnotationAssertion(rdfs:label "obliquely striated muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (carbohydrate secreting cell) @@ -17324,34 +16493,41 @@ SubClassOf( (biogenic amine secreting cell) +AnnotationAssertion(Annotation( ) "ZFA:0009212") AnnotationAssertion(rdfs:label "biogenic amine secreting cell") SubClassOf( ) # Class: (serotonin secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:19630576") "A cell type that secretes 5-Hydroxytryptamine (serotonin).") +AnnotationAssertion(Annotation( ) "ZFA:0009213") AnnotationAssertion( "5-HT secreting cell") AnnotationAssertion( "5-Hydroxytryptamine secreting cell") AnnotationAssertion(rdfs:label "serotonin secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (noradrenergic cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:068340007X") "A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme.") +AnnotationAssertion(Annotation( ) "ZFA:0009214") AnnotationAssertion( "noradrenaline secreting cell") AnnotationAssertion( "norepinephrin secreting cell") AnnotationAssertion( "norepinephrine secreting cell") AnnotationAssertion(rdfs:label "noradrenergic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (visible light photoreceptor cell) AnnotationAssertion(Annotation( "GOC:tfm") "A photoreceptor cell that detects visible light.") +AnnotationAssertion(Annotation( ) "ZFA:0009219") AnnotationAssertion(rdfs:label "visible light photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stromal cell) @@ -17359,10 +16535,12 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0002064") AnnotationAssertion( "FMA:83624") +AnnotationAssertion(Annotation( ) "ZFA:0009226") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stromal cell") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -17370,37 +16548,49 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "MESH:D032386") "A precursor cell destined to differentiate into cardiac muscle cell.") AnnotationAssertion( "FMA:84797") +AnnotationAssertion(Annotation( ) "ZFA:0009234") AnnotationAssertion( "cardiac muscle progenitor cell") AnnotationAssertion( "cardiomyocyte progenitor cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle myoblast) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "MESH:D032390") "A precursor cell destined to differentiate into smooth muscle myocytes.") AnnotationAssertion( "FMA:84798") +AnnotationAssertion(Annotation( ) "ZFA:0009235") AnnotationAssertion(Annotation( "MESH:D032390") "myoblast, smooth muscle") AnnotationAssertion( "satellite cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle myoblast) AnnotationAssertion(Annotation( "SANBI:mhl") "A myoblast that differentiates into skeletal muscle fibers.") AnnotationAssertion( "FMA:84799") +AnnotationAssertion(Annotation( ) "ZFA:0009236") AnnotationAssertion( "skeletal myoblast") AnnotationAssertion(rdfs:label "skeletal muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fungal cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that only exists in Fungi.") AnnotationAssertion(rdfs:label "fungal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (syncytiotrophoblast cell) @@ -17416,6 +16606,8 @@ AnnotationAssertion( "syncytiotrophoblast cell") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/2100") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (afferent neuron) @@ -17423,6 +16615,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "MESH:D009475") "A neuron which conveys sensory information centrally from the periphery.") AnnotationAssertion( ) AnnotationAssertion( "FMA:87653") +AnnotationAssertion(Annotation( ) "ZFA:0009238") AnnotationAssertion( "input neuron") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "afferent neuron") @@ -17431,6 +16624,7 @@ SubClassOf( (efferent neuron) AnnotationAssertion(Annotation( "MESH:D009476") "A neuron which sends impulses peripherally to activate muscles or secretory cells.") +AnnotationAssertion(Annotation( ) "ZFA:0009239") AnnotationAssertion( "output neuron") AnnotationAssertion(rdfs:label "efferent neuron") SubClassOf( ) @@ -17441,10 +16635,11 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0000938") AnnotationAssertion( "CALOHA:TS-0683") -AnnotationAssertion( "FBbt:00005106") +AnnotationAssertion(Annotation( ) "FBbt:00005106") AnnotationAssertion( "FMA:54527") AnnotationAssertion( "VHOG:0001483") AnnotationAssertion( "WBbt:0003679") +AnnotationAssertion(Annotation( ) "ZFA:0009248") AnnotationAssertion( "nerve cell") AnnotationAssertion( ) AnnotationAssertion( ) @@ -17466,12 +16661,16 @@ AnnotationAssertion( "FMA:62863") AnnotationAssertion( "MESH:D008214") AnnotationAssertion( "VHOG:0001535") +AnnotationAssertion(Annotation( ) "ZFA:0009250") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)") AnnotationAssertion(rdfs:label "lymphocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -17486,12 +16685,29 @@ AnnotationAssertion( "proerythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (basophilic erythroblast) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721601464") "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.") AnnotationAssertion( "FMA:83505") +AnnotationAssertion(Annotation( ) "ZFA:0005236") AnnotationAssertion(Annotation( "ISBN:0721601464") "basophilic normoblast") AnnotationAssertion(Annotation( "ISBN:0721601464") "early erythroblast") AnnotationAssertion(Annotation( "ISBN:0721601464") "early normoblast") @@ -17499,12 +16715,15 @@ AnnotationAssertion(Annotation( "basophilic erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (polychromatophilic erythroblast) AnnotationAssertion(Annotation( "ISBN:0721601464") "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.") AnnotationAssertion( "FMA:83506") +AnnotationAssertion(Annotation( ) "ZFA:0005241") AnnotationAssertion(Annotation( "ISBN:0721601464") "intermediate erythroblast") AnnotationAssertion(Annotation( "ISBN:0721601464") "intermediate normoblast") AnnotationAssertion(Annotation( "ISBN:0721601464") "polychromatic erythroblast") @@ -17514,6 +16733,9 @@ AnnotationAssertion(Annotation( "polychromatophilic erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (orthochromatic erythroblast) @@ -17528,6 +16750,8 @@ AnnotationAssertion(Annotation( "orthochromatic erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (megakaryocyte progenitor cell) @@ -17553,8 +16777,23 @@ AnnotationAssertion( "Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative.") AnnotationAssertion(rdfs:label "megakaryocyte progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (megakaryocyte) @@ -17582,41 +16821,65 @@ AnnotationAssertion(Annotation( "BTO:0001173") AnnotationAssertion( "CALOHA:TS-0864") AnnotationAssertion( "MESH:D012156") +AnnotationAssertion(Annotation( ) "ZFA:0009252") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reticulocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (nucleate erythrocyte) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOc:tfm") "An erythrocyte having a nucleus.") AnnotationAssertion( "RBC") AnnotationAssertion( "red blood cell") +AnnotationAssertion(Annotation( ) "ZFA:0009256") AnnotationAssertion(rdfs:label "nucleate erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (angioblastic mesenchymal cell) AnnotationAssertion(Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "PMID:12768659") "A mesenchymal stem cell capable of developing into blood vessel endothelium.") +AnnotationAssertion(Annotation( ) "ZFA:0009258") AnnotationAssertion( "angioblast") AnnotationAssertion( "chondroplast") AnnotationAssertion(rdfs:comment "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.") AnnotationAssertion(rdfs:label "angioblastic mesenchymal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac mesenchymal cell) AnnotationAssertion(Annotation( "PMID:18816864") "A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field.") +AnnotationAssertion(Annotation( ) "ZFA:0009259") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac mesenchymal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (retinal cone cell) @@ -17625,6 +16888,7 @@ AnnotationAssertion( "BTO:0001036") AnnotationAssertion( "CALOHA:TS-0866") AnnotationAssertion( "FMA:67748") +AnnotationAssertion(Annotation( ) "ZFA:0009262") AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") "cone") AnnotationAssertion( ) AnnotationAssertion( ) @@ -17639,13 +16903,16 @@ AnnotationAssertion( "BTO:0004298") AnnotationAssertion( "CALOHA:TS-0173") AnnotationAssertion( "FMA:70551") +AnnotationAssertion(Annotation( ) "ZFA:0009264") AnnotationAssertion(Annotation( "FMA:70551") "epithelial cell of cornea") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "corneal epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (germ cell) @@ -17662,8 +16929,11 @@ SubClassOf( ObjectSomeValuesFrom( (androgen secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") "A steroid hormone secreting cell that secretes androgen.") +AnnotationAssertion(Annotation( ) "ZFA:0009271") AnnotationAssertion(rdfs:label "androgen secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (enucleate erythrocyte) @@ -17673,6 +16943,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "enucleate erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -17683,12 +16954,15 @@ AnnotationAssertion( "FMA:67310") AnnotationAssertion( "FMA:86775") AnnotationAssertion( "NIFSTD:sao862606388") +AnnotationAssertion(Annotation( ) "ZFA:0009273") AnnotationAssertion( "projection neuron") AnnotationAssertion( "pyramidal cell") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (retinal rod cell) @@ -17697,6 +16971,7 @@ AnnotationAssertion( "BTO:0001024") AnnotationAssertion( "CALOHA:TS-0870") AnnotationAssertion( "FMA:67747") +AnnotationAssertion(Annotation( ) "ZFA:0009275") AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") "rod") AnnotationAssertion( ) AnnotationAssertion( ) @@ -17708,6 +16983,7 @@ SubClassOf( ObjectSomeValuesFrom( "FB:ma") Annotation( "GOC:tfm") "A cell whose primary function is to support other cell types.") AnnotationAssertion( "BTO:0002315") +AnnotationAssertion(Annotation( ) "ZFA:0009387") AnnotationAssertion( "supportive cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "supporting cell") @@ -17716,6 +16992,7 @@ SubClassOf( (collagen secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") "An extracellular matrix secreting cell that secretes collagen.") +AnnotationAssertion(Annotation( ) "ZFA:0009287") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "collagen secreting cell") SubClassOf( ) @@ -17724,6 +17001,7 @@ SubClassOf( "GOC:tfm") Annotation( "PMID:1381289") "A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.") AnnotationAssertion( "FMA:70567") +AnnotationAssertion(Annotation( ) "ZFA:0009288") AnnotationAssertion( "gonocyte") AnnotationAssertion( "primitive germ cell") AnnotationAssertion( ) @@ -17731,6 +17009,7 @@ AnnotationAssertion(rdfs:label "prim EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female gamete) @@ -17742,27 +17021,39 @@ SubClassOf( (muscle precursor cell) AnnotationAssertion(Annotation( "GOC:add") "A non-terminally differentiated cell that is capable of developing into a muscle cell.") +AnnotationAssertion(Annotation( ) "ZFA:0009291") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle precursor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stellate interneuron) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any interneuron that has characteristic some stellate morphology.") +AnnotationAssertion(Annotation( ) "ZFA:0009297") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stellate interneuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neurogliaform cell) AnnotationAssertion(Annotation( "JB:jb") Annotation( "PMID:17122314") "An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts.") +AnnotationAssertion(Annotation( ) "ZFA:0009299") AnnotationAssertion(Annotation( "PMID:18568015") "NGF cell") AnnotationAssertion(Annotation( "PMID:3235828") "neuroglioform cell") AnnotationAssertion( "spiderweb cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neurogliaform cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (PP cell) @@ -17785,14 +17076,19 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "neurecto-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatic stem cell) AnnotationAssertion(Annotation( "GO:0048103") "A stem cell that can give rise to cell types of the body other than those of the germ-line.") AnnotationAssertion( "CALOHA:TS-2086") AnnotationAssertion( "MESH:D053687") +AnnotationAssertion(Annotation( ) "ZFA:0009307") AnnotationAssertion(rdfs:label "somatic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (striated muscle cell) @@ -17800,9 +17096,12 @@ AnnotationAssertion(Annotation( "BTO:0002916") AnnotationAssertion( "CALOHA:TS-2157") AnnotationAssertion( "FMA:86936") +AnnotationAssertion(Annotation( ) "ZFA:0005784") AnnotationAssertion(rdfs:label "striated muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (leukocyte) @@ -17814,6 +17113,7 @@ AnnotationAssertion( "FMA:62852") AnnotationAssertion( "MESH:D007962") AnnotationAssertion( "NCIT:C12529") +AnnotationAssertion(Annotation( ) "ZFA:0009309") AnnotationAssertion( "leucocyte") AnnotationAssertion( "white blood cell") AnnotationAssertion( "immune cell") @@ -17821,10 +17121,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "leukocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (retinal ganglion cell) @@ -17833,6 +17138,7 @@ AnnotationAssertion( "BTO:0001800") AnnotationAssertion( "FMA:67765") AnnotationAssertion( "MESH:D012165") +AnnotationAssertion(Annotation( ) "ZFA:0009310") AnnotationAssertion( "gangliocyte") AnnotationAssertion( "ganglion cell of retina") AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "RGC") @@ -17854,6 +17160,7 @@ AnnotationAssertion( "CALOHA:TS-0115") AnnotationAssertion( "FMA:14067") AnnotationAssertion( "MESH:D032383") +AnnotationAssertion(Annotation( ) "ZFA:0009316") AnnotationAssertion(Annotation( "GO:0048739") "cardiac muscle fiber") AnnotationAssertion( "cardiac myocyte") AnnotationAssertion( "cardiomyocyte") @@ -17864,6 +17171,10 @@ AnnotationAssertion( "This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction.") AnnotationAssertion(rdfs:label "cardiac muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (myeloid cell) @@ -17872,10 +17183,13 @@ AnnotationAssertion(Annotation( "BTO:0001441") AnnotationAssertion( "CALOHA:TS-0647") AnnotationAssertion( "MESH:D022423") +AnnotationAssertion(Annotation( ) "ZFA:0009324") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myeloid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (erythroid lineage cell) @@ -17884,6 +17198,7 @@ AnnotationAssertion( "CALOHA:TS-0290") AnnotationAssertion( "FMA:62845") AnnotationAssertion( "FMA:83516") +AnnotationAssertion(Annotation( ) "ZFA:0009325") AnnotationAssertion( "erythropoietic cell") AnnotationAssertion( ) AnnotationAssertion( ) @@ -17898,21 +17213,39 @@ AnnotationAssertion( "CALOHA:TS-0289") AnnotationAssertion( "FMA:83504") AnnotationAssertion( "MESH:D004900") +AnnotationAssertion(Annotation( ) "ZFA:0005237") AnnotationAssertion( "normoblast") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myeloid leukocyte) AnnotationAssertion(Annotation( "GOC:add") "A cell of the monocyte, granulocyte, or mast cell lineage.") +AnnotationAssertion(Annotation( ) "ZFA:0009326") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myeloid leukocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) # Class: (hematopoietic multipotent progenitor cell) @@ -17920,6 +17253,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0000725") AnnotationAssertion( "CALOHA:TS-0448") +AnnotationAssertion(Annotation( ) "ZFA:0009354") AnnotationAssertion( "MPP") AnnotationAssertion( "hemopoietic progenitor cell") AnnotationAssertion( ) @@ -17928,8 +17262,23 @@ 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(Annotation( "true") ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -17940,11 +17289,14 @@ AnnotationAssertion( "BTO:0004731") AnnotationAssertion( "CALOHA:TS-2025") AnnotationAssertion( "FMA:70338") +AnnotationAssertion(Annotation( ) "ZFA:0009355") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this is a class of cell types, not an identified single cell type.") AnnotationAssertion(rdfs:label "lymphoid lineage restricted progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (myeloid lineage restricted progenitor cell) @@ -17955,12 +17307,15 @@ AnnotationAssertion( "BTO:0004730") AnnotationAssertion( "CALOHA:TS-2099") AnnotationAssertion( "FMA:70339") +AnnotationAssertion(Annotation( ) "ZFA:0009356") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this is a class of cell types, not an identified single cell type.") AnnotationAssertion(rdfs:label "myeloid lineage restricted progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mononuclear cell) @@ -17968,26 +17323,31 @@ AnnotationAssertion(Annotation( "BTO:0000878") AnnotationAssertion( "CALOHA:TS-0768") AnnotationAssertion( "FMA:86713") +AnnotationAssertion(Annotation( ) "ZFA:0009357") AnnotationAssertion( "mononuclear leukocyte") AnnotationAssertion( "peripheral blood mononuclear cell") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mononuclear cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) # Class: (serotonergic neuron) AnnotationAssertion(Annotation( "SANBI:mhl") "A neuron that releases serotonin as a neurotransmitter.") -AnnotationAssertion( "FBbt:00005133") +AnnotationAssertion(Annotation( ) "FBbt:00005133") AnnotationAssertion( "MESH:D059326") AnnotationAssertion( "WBbt:0006837") +AnnotationAssertion(Annotation( ) "ZFA:0009361") AnnotationAssertion( "5-HT neuron") AnnotationAssertion( "5-hydroxytryptamine neuron") AnnotationAssertion( "serotinergic neuron") AnnotationAssertion(rdfs:label "serotonergic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hematopoietic cell) @@ -17996,6 +17356,7 @@ AnnotationAssertion( "CALOHA:TS-2017") AnnotationAssertion( "FMA:70366") AnnotationAssertion( "FMA:83598") +AnnotationAssertion(Annotation( ) "ZFA:0005830") AnnotationAssertion( "haematopoietic cell") AnnotationAssertion( "haemopoietic cell") AnnotationAssertion( "hemopoietic cell") @@ -18013,6 +17374,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hematopoietic oligopotent progenitor cell, lineage-negative) @@ -18022,8 +17385,18 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "hematopoietic oligopotent progenitor cell, lineage-negative") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abnormal cell) @@ -18036,6 +17409,7 @@ AnnotationAssertion(rdfs:comment "ht AnnotationAssertion(rdfs:label "abnormal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neoplastic cell) @@ -18050,6 +17424,7 @@ AnnotationAssertion(rdfs:comment "ht AnnotationAssertion(rdfs:label "neoplastic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (malignant cell) @@ -18063,6 +17438,7 @@ AnnotationAssertion(rdfs:comment "ht AnnotationAssertion(rdfs:label "malignant cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (erythroid progenitor cell, mammalian) @@ -18078,6 +17454,19 @@ AnnotationAssertion( "erythroid progenitor cell, mammalian") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hematopoietic lineage restricted progenitor cell) @@ -18087,8 +17476,9 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hematopoietic lineage restricted progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -18101,8 +17491,9 @@ 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(Annotation( "true") ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (type A enteroendocrine cell) @@ -18113,6 +17504,8 @@ AnnotationAssertion( AnnotationAssertion( "FMA:62939") AnnotationAssertion(rdfs:label "type A enteroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (Purkinje myocyte) @@ -18168,7 +17561,9 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-06-29T03:38:14Z") AnnotationAssertion( "FMA:69075") +AnnotationAssertion(Annotation( ) "ZFA:0009383") AnnotationAssertion(rdfs:label "endo-epithelial cell") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -18178,8 +17573,12 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-06-29T03:38:22Z") AnnotationAssertion( "FMA:69074") +AnnotationAssertion(Annotation( ) "ZFA:0009385") AnnotationAssertion(rdfs:label "ecto-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (meso-epithelial cell) @@ -18187,9 +17586,13 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-06-29T03:49:14Z") AnnotationAssertion( "FMA:69076") +AnnotationAssertion(Annotation( ) "ZFA:0009388") AnnotationAssertion( "epithelial mesenchymal cell") AnnotationAssertion(rdfs:label "meso-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (specialized cardiac myocyte) @@ -18211,6 +17614,7 @@ AnnotationAssertion( "nongranular leukocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone marrow cell) @@ -18225,6 +17629,7 @@ AnnotationAssertion(rdfs:comment "MH AnnotationAssertion(rdfs:label "bone marrow cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hilus cell of ovary) @@ -18249,6 +17654,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "stromal cell of ovary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell of vascular tree) @@ -18278,7 +17685,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capillary endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (general ecto-epithelial cell) @@ -18298,6 +17706,7 @@ AnnotationAssertion( "epithelial cell of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucous cell of stomach) @@ -18307,8 +17716,8 @@ AnnotationAssertion( AnnotationAssertion( "FMA:63464") AnnotationAssertion(rdfs:label "mucous cell of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stem cell of gastric gland) @@ -18319,7 +17728,9 @@ AnnotationAssertion( "stem cell of gastric gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vertebrate lens cell) @@ -18346,6 +17757,7 @@ AnnotationAssertion(rdfs:label "lens EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (marrow fibroblast) @@ -18356,6 +17768,7 @@ AnnotationAssertion( "marrow fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (nucleate cell) @@ -18365,6 +17778,8 @@ AnnotationAssertion( AnnotationAssertion( "FMA:67513") AnnotationAssertion(rdfs:label "nucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (peripheral blood stem cell) @@ -18378,6 +17793,8 @@ AnnotationAssertion( "peripheral blood stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of alimentary canal) @@ -18387,6 +17804,7 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "epithelial cell of alimentary canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of esophagus) @@ -18394,10 +17812,12 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-09-08T09:28:20Z") AnnotationAssertion( "FMA:63071") +AnnotationAssertion(Annotation( ) "ZFA:0009400") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell of sinusoid) @@ -18410,6 +17830,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endothelial cell of sinusoid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (type A cell of stomach) @@ -18420,6 +17842,7 @@ AnnotationAssertion( "type A cell of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (epithelial cell of skin gland) @@ -18431,6 +17854,7 @@ AnnotationAssertion( "epithelial cell of skin gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural cell) @@ -18442,6 +17866,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (connective tissue cell) @@ -18451,9 +17877,12 @@ AnnotationAssertion( AnnotationAssertion( "CALOHA:TS-2096") AnnotationAssertion( "FMA:63875") AnnotationAssertion( "MESH:D003239") +AnnotationAssertion(Annotation( ) "ZFA:0009392") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "connective tissue cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic cell (metazoa)) @@ -18463,6 +17892,7 @@ AnnotationAssertion( AnnotationAssertion( "CALOHA:TS-0263") AnnotationAssertion( "FMA:82840") AnnotationAssertion( "WBbt:0007028") +AnnotationAssertion(Annotation( ) "ZFA:0007089") AnnotationAssertion(rdfs:label "embryonic cell (metazoa)") SubClassOf( ) @@ -18473,6 +17903,7 @@ AnnotationAssertion( "2010-09-20T02:25:25Z") AnnotationAssertion(rdfs:label "neural crest derived adipocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (endocardial cell) @@ -18488,7 +17919,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocardial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (gestational hematopoietic stem cell) @@ -18498,6 +17930,7 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "gestational hematopoietic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (keratocyte) @@ -18512,8 +17945,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "keratocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory epithelial cell) @@ -18526,17 +17959,21 @@ AnnotationAssertion( "respiratory epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (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( ) AnnotationAssertion( "2010-09-24T01:13:01Z") -AnnotationAssertion( "FBbt:00005812") +AnnotationAssertion(Annotation( ) "FBbt:00005812") AnnotationAssertion( "myotubule") AnnotationAssertion( "single cell sarcomere") AnnotationAssertion(rdfs:label "myotube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Schwann cell precursor) @@ -18547,6 +17984,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "Schwann cell precursor") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (immature Schwann cell) @@ -18555,7 +17993,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-09-24T02:10:31Z") AnnotationAssertion( "Schwann cell") -AnnotationAssertion( "ZFA:0001725") +AnnotationAssertion(Annotation( ) "ZFA:0001725") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "immature Schwann cell") SubClassOf( ) @@ -18569,6 +18007,7 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "nucleated reticulocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) # Class: (enucleated reticulocyte) @@ -18580,7 +18019,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enucleated reticulocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (oligodendrocyte precursor cell) @@ -18597,9 +18038,9 @@ 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( ))) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiocyte) @@ -18614,6 +18055,8 @@ 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( ObjectSomeValuesFrom( )) # Class: (adventitial cell) @@ -18627,6 +18070,7 @@ AnnotationAssertion(rdfs:label "adve EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (subcutaneous adipocyte) @@ -18640,6 +18084,7 @@ AnnotationAssertion( "subcutaneous adipocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (aortic smooth muscle cell) @@ -18650,7 +18095,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aortic smooth muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchymal stem cell of the bone marrow) @@ -18659,6 +18105,8 @@ AnnotationAssertion( "2011-02-28T01:47:47Z") AnnotationAssertion(rdfs:label "mesenchymal stem cell of the bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (vein endothelial cell) @@ -18675,12 +18123,14 @@ AnnotationAssertion( "vein endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +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") +AnnotationAssertion(Annotation( ) "ZFA:0005773") AnnotationAssertion(rdfs:comment "See CL:0002619.") AnnotationAssertion(rdfs:label "embryonic blood vessel endothelial progenitor cell") SubClassOf( ) @@ -18693,6 +18143,7 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "fibroblast of the aortic adventitia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of cardiac tissue) @@ -18705,14 +18156,17 @@ AnnotationAssertion(rdfs:label "fibr EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of dermis) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any skin fibroblast that is part of some dermis.") AnnotationAssertion( ) AnnotationAssertion( "2011-02-28T05:05:33Z") AnnotationAssertion(rdfs:label "fibroblast of dermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of lung) @@ -18725,6 +18179,7 @@ AnnotationAssertion( "fibroblast of lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of pulmonary artery) @@ -18736,6 +18191,7 @@ AnnotationAssertion( "fibroblast of pulmonary artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchymal stem cell of adipose tissue) @@ -18746,6 +18202,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchymal stem cell of adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Schwann cell) @@ -18775,6 +18233,8 @@ AnnotationAssertion( "retinal blood vessel endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell of the brachiocephalic vasculature) @@ -18783,7 +18243,8 @@ AnnotationAssertion( "2011-03-06T05:00:58Z") AnnotationAssertion(rdfs:label "smooth muscle cell of the brachiocephalic vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell of the brain vasculature) @@ -18793,6 +18254,8 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "smooth muscle cell of the brain vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell of the pulmonary artery) @@ -18805,7 +18268,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle cell of the pulmonary artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell of the subclavian artery) @@ -18814,7 +18278,8 @@ AnnotationAssertion( "2011-03-06T05:01:52Z") AnnotationAssertion(rdfs:label "smooth muscle cell of the subclavian artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell of the carotid artery) @@ -18823,7 +18288,8 @@ AnnotationAssertion( "2011-03-06T05:01:56Z") AnnotationAssertion(rdfs:label "smooth muscle cell of the carotid artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell of the esophagus) @@ -18833,6 +18299,7 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "smooth muscle cell of the esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (raphe nuclei neuron) @@ -18842,6 +18309,8 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "raphe nuclei neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuron of the ventral spinal cord) @@ -18851,6 +18320,8 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "neuron of the ventral spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin fibroblast) @@ -18865,15 +18336,18 @@ AnnotationAssertion( "skin fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of lower respiratory tract) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any respiratory epithelial cell that is part of some lower respiratory tract.") AnnotationAssertion( ) AnnotationAssertion( "2011-06-21T12:29:31Z") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of lower respiratory tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (glandular cell of esophagus) @@ -18897,6 +18371,7 @@ AnnotationAssertion( "glandular cell of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) # Class: (myocardial endocrine cell of atrium) @@ -18907,6 +18382,7 @@ AnnotationAssertion( "myocardial endocrine cell of atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardioblast) @@ -18925,6 +18401,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2011-08-16T02:38:01Z") AnnotationAssertion(rdfs:label "retinal progenitor cell") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -18936,6 +18413,8 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tongue muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural crest derived neuroblast) @@ -18944,6 +18423,7 @@ AnnotationAssertion( "2011-08-22T09:24:15Z") AnnotationAssertion(rdfs:label "neural crest derived neuroblast") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bistratified retinal ganglion cell) @@ -18956,6 +18436,8 @@ AnnotationAssertion( "CL:0003001") AnnotationAssertion(rdfs:label "bistratified retinal ganglion cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (monostratified cell) @@ -18966,6 +18448,8 @@ AnnotationAssertion( "CL:0004246") AnnotationAssertion(rdfs:label "monostratified cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bistratified cell) @@ -18975,22 +18459,29 @@ AnnotationAssertion( "CL:0004247") AnnotationAssertion(rdfs:label "bistratified cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord interneuron) AnnotationAssertion(Annotation( "CL:CVS") "A CNS interneuron located in the spinal cord.") +AnnotationAssertion(Annotation( ) "ZFA:0000778") AnnotationAssertion(rdfs:comment "Is_a interneuron, part_of UBERON:0002240.") AnnotationAssertion(rdfs:label "spinal cord interneuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatomotor neuron) AnnotationAssertion(Annotation( "ZFIN:CVS") "A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic.") +AnnotationAssertion(Annotation( ) "ZFA:0005733") AnnotationAssertion( "somatic motor neuron") AnnotationAssertion(rdfs:label "somatomotor neuron"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletogenic cell) @@ -19007,7 +18498,9 @@ SubClassOf( "UBERONREF:0000002") "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.") AnnotationAssertion( ) AnnotationAssertion( "2012-06-27T08:27:35Z") +AnnotationAssertion(Annotation( ) "ZFA:0007084") AnnotationAssertion(rdfs:label "premigratory neural crest cell") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -19040,26 +18533,34 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeletal muscle fiber"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (visceral muscle cell) AnnotationAssertion(Annotation( "GOC:dos") "A muscle cell that is part of some visceral muscle.") -AnnotationAssertion( "FBbt:00005070") +AnnotationAssertion(Annotation( ) "FBbt:00005070") AnnotationAssertion(rdfs:label "visceral muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (striated visceral muscle cell) AnnotationAssertion(Annotation( "GOC:dos") "A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods.") AnnotationAssertion(rdfs:label "striated visceral muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) +SubClassOf( ) # Class: (transversely striated visceral muscle cell) AnnotationAssertion(Annotation( "GOC:dos") "A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods.") AnnotationAssertion(rdfs:label "transversely striated visceral muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (adult skeletal muscle myoblast) @@ -19068,6 +18569,8 @@ AnnotationAssertion(Annotation( "The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins.") AnnotationAssertion(rdfs:label "adult skeletal muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (mesenchymal cell) @@ -19077,7 +18580,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchymal cell") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -19086,19 +18589,29 @@ SubClassOf( ObjectSomeValuesFrom( "PMID:18816864") "A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves.") AnnotationAssertion(rdfs:label "endocardial cushion cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (noradrenergic neuron) AnnotationAssertion(Annotation( "GOC:dos") "A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter.") +AnnotationAssertion(Annotation( ) "ZFA:0005873") AnnotationAssertion(rdfs:label "noradrenergic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (visual system neuron) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any neuron that is capable of part of some visual perception.") AnnotationAssertion( ) AnnotationAssertion( "2017-07-09T19:12:36Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "visual system neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cortical interneuron) @@ -19107,6 +18620,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cortical interneuron"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (mural cell) @@ -19114,6 +18629,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( "2020-02-29T17:33:55Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( ) "ZFA:0005944") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -19122,11 +18638,14 @@ SubClassOf( (microcirculation associated smooth muscle cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any vascular associated smooth muscle cell that is part of some microcirculatory vessel.") AnnotationAssertion( ) AnnotationAssertion( "2020-02-29T17:37:00Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "microcirculation associated smooth muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sensory neuron of spinal nerve) @@ -19134,7 +18653,8 @@ AnnotationAssertion(Annotation( "spinal sensory neuron") AnnotationAssertion(rdfs:label "sensory neuron of spinal nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (compound eye retinal cell) @@ -19143,6 +18663,8 @@ AnnotationAssertion( "PMID:12021768") AnnotationAssertion(rdfs:label "compound eye retinal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (retinal cell) @@ -19152,6 +18674,7 @@ AnnotationAssertion( "retinal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic skeletal muscle fiber) @@ -19160,6 +18683,8 @@ AnnotationAssertion( "2022-02-21T15:39:10Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "embryonic skeletal muscle fiber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stromal cell of bone marrow) @@ -19168,6 +18693,8 @@ AnnotationAssertion( "bone marrow stromal cell") AnnotationAssertion(rdfs:label "stromal cell of bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (mononuclear cell of bone marrow) @@ -19176,30 +18703,47 @@ AnnotationAssertion( "bone marrow mononuclear cell") AnnotationAssertion(rdfs:label "mononuclear cell of bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (cardiac blood vessel endothelial cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any blood vessel endothelial cell that is part of some heart.") AnnotationAssertion(rdfs:label "cardiac blood vessel endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (His-Purkinje system cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that is part of some His-Purkinje system.") AnnotationAssertion(rdfs:label "His-Purkinje system cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac endothelial cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any endothelial cell that is part of some heart.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (camera-type eye photoreceptor cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any photoreceptor cell that is part of some camera-type eye.") AnnotationAssertion( "camera type eye photoreceptor cell") AnnotationAssertion(rdfs:label "camera-type eye photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf(Annotation(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/2245") ObjectSomeValuesFrom( )) # Class: (cerebral cortex neuron) @@ -19215,6 +18759,8 @@ AnnotationAssertion( "cerebral cortex neuron") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/1359") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (zygote) @@ -19226,14 +18772,21 @@ SubClassOf( (cardiac glial cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any glial cell that is part of some heart.") AnnotationAssertion(rdfs:label "cardiac glial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac myoblast) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any myoblast that develops into some cardiac muscle cell.") AnnotationAssertion( "MESH:D032386") AnnotationAssertion(rdfs:label "cardiac myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac neuron) @@ -19243,6 +18796,8 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "cardiac neuron") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/pull/1488") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord motor neuron) @@ -19250,6 +18805,8 @@ AnnotationAssertion(Annotation( "spinal cord motor neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (paraxial cell) @@ -19260,6 +18817,7 @@ AnnotationAssertion( "paraxial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural crest cell) @@ -19277,6 +18835,8 @@ AnnotationAssertion( "mesothelial cell of epicardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of upper back skin) @@ -19285,6 +18845,7 @@ AnnotationAssertion( "fibroblast of upper back skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of skin of back) @@ -19292,7 +18853,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fibroblast of skin of back") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (progenitor cell) @@ -19301,7 +18863,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle fibroblast) @@ -19311,7 +18875,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeletal muscle fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (dermal microvascular endothelial cell) @@ -19321,6 +18886,8 @@ AnnotationAssertion( "dermal microvascular endothelium cell") AnnotationAssertion(rdfs:label "dermal microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (precursor cell) @@ -19329,6 +18896,8 @@ AnnotationAssertion( "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.") AnnotationAssertion(rdfs:label "precursor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuron of the forebrain) @@ -19340,6 +18909,8 @@ AnnotationAssertion( "neuron of the forebrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neutrophillic cytoplasm) @@ -19348,6 +18919,8 @@ AnnotationAssertion( "2010-05-25T01:36:34Z") AnnotationAssertion(rdfs:label "neutrophillic cytoplasm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acidophilic cytoplasm) @@ -19357,6 +18930,8 @@ AnnotationAssertion( AnnotationAssertion( "eosinophilic") AnnotationAssertion(rdfs:label "acidophilic cytoplasm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (basophilic cytoplasm) @@ -19366,6 +18941,7 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "basophilic cytoplasm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (polychromatophilic cytoplasm) @@ -19374,6 +18950,8 @@ AnnotationAssertion( "2009-12-28T04:25:23Z") AnnotationAssertion(rdfs:label "polychromatophilic cytoplasm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (reniform nucleus) @@ -19383,12 +18961,15 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "reniform nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (alobate nucleus) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any nucleus that has characteristic some alobate.") AnnotationAssertion(rdfs:label "alobate nucleus"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vessel smooth muscle cell) @@ -19400,16 +18981,26 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood vessel smooth muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (forebrain neuroblast) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any neuroblast (sensu Vertebrata) that is part of some forebrain.") AnnotationAssertion(rdfs:label "forebrain neuroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stomach neuroendocrine cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any neuroendocrine cell that is part of some stomach.") AnnotationAssertion(rdfs:label "stomach neuroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (lung neuroendocrine cell) @@ -19421,25 +19012,35 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung neuroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung ciliated cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any ciliated cell that is part of some lung.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung ciliated cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung secretory cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is part of some lung.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung secretory cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (trophectodermal cell) @@ -19454,6 +19055,9 @@ AnnotationAssertion( "FMA:256516") "squamous mesothelial cell of dura mater") AnnotationAssertion(rdfs:label "mesothelial cell of dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of areolar connective tissue) @@ -19471,6 +19075,8 @@ AnnotationAssertion( "fibroblast of tunica adventitia of artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of dense regular elastic tissue) @@ -19480,6 +19086,7 @@ AnnotationAssertion(rdfs:label "fibr EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (epicardial adipocyte) @@ -19492,6 +19099,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epicardial adipocyte") SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (adipocyte of epicardial fat of right ventricle) @@ -19502,7 +19110,7 @@ AnnotationAssertion(Annotation( "FMA:261297") "epicardial fat cell of right ventricle") AnnotationAssertion(rdfs:label "adipocyte of epicardial fat of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (adipocyte of epicardial fat of left ventricle) @@ -19514,7 +19122,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "adipocyte of epicardial fat of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (transitional myocyte of interatrial septum) @@ -19524,6 +19132,8 @@ AnnotationAssertion( "transitional myocyte of interatrial septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (transitional myocyte of interventricular septum) @@ -19532,6 +19142,8 @@ AnnotationAssertion( "transitional myocyte of interventricular septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (Purkinje myocyte of interventricular septum) @@ -19540,6 +19152,8 @@ AnnotationAssertion( "Purkinje myocyte of interventricular septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myocyte of sinoatrial node) @@ -19553,6 +19167,8 @@ AnnotationAssertion(Annotation( "myocyte of sinoatrial node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myocyte of atrioventricular node) @@ -19566,6 +19182,9 @@ AnnotationAssertion(Annotation( "myocyte of atrioventricular node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell of arteriole) @@ -19577,6 +19196,7 @@ AnnotationAssertion( "endothelial cell of arteriole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell of artery) @@ -19603,16 +19223,19 @@ AnnotationAssertion( "endothelial cell of venule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stem cell of epidermis) AnnotationAssertion(Annotation( "GOC:tfm") "A somatic stem cell that is part of the epidermis.") AnnotationAssertion( "FMA:70541") +AnnotationAssertion(Annotation( ) "ZFA:0007122") AnnotationAssertion(Annotation( "FMA:70541") "epidermal stem cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stem cell of epidermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ciliary muscle cell) @@ -19624,6 +19247,7 @@ AnnotationAssertion( "ciliary muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of anterior chamber of eye) @@ -19631,6 +19255,8 @@ AnnotationAssertion(Annotation( "FMA:70615") AnnotationAssertion(rdfs:label "mesothelial cell of anterior chamber of eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of parietal peritoneum) @@ -19638,6 +19264,8 @@ AnnotationAssertion(Annotation( "FMA:72142") AnnotationAssertion(rdfs:label "mesothelial cell of parietal peritoneum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of visceral peritoneum) @@ -19647,6 +19275,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell of visceral peritoneum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (transitional myocyte of sinoatrial node) @@ -19656,6 +19286,7 @@ AnnotationAssertion( "transitional myocyte of sinoatrial node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) # Class: (Purkinje myocyte of atrioventricular node) @@ -19664,6 +19295,7 @@ AnnotationAssertion( "Purkinje myocyte of atrioventricular node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) # Class: (myocardial endocrine cell of interventricular septum) @@ -19672,6 +19304,8 @@ AnnotationAssertion( "myocardial endocrine cell of interventricular septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of peritoneum) @@ -19680,6 +19314,8 @@ AnnotationAssertion( "FMA:86736") "peritoneal mesothelial cell") AnnotationAssertion(rdfs:label "mesothelial cell of peritoneum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of pleura) @@ -19689,6 +19325,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "mesothelial cell of pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of parietal pleura) @@ -19696,6 +19334,8 @@ AnnotationAssertion(Annotation( "FMA:86738") AnnotationAssertion(rdfs:label "mesothelial cell of parietal pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of visceral pleura) @@ -19706,17 +19346,24 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell of visceral pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung endothelial cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any endothelial cell of vascular tree that is part of some lung.") AnnotationAssertion( "endothelial cell of lung") AnnotationAssertion( "pulmonary vessel endothelial cell") AnnotationAssertion(rdfs:label "lung endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary artery endothelial cell) +AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any endothelial cell of vascular tree that is part of some pulmonary artery.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0001141") AnnotationAssertion(Annotation( "BTO:0001141") "PAEC cell") @@ -19724,6 +19371,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary artery endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (oral mucosa squamous cell) @@ -19736,6 +19384,9 @@ AnnotationAssertion(Annotation( "CALOHA:TS-1252") "oral mucosa squamous epithelial cells") AnnotationAssertion(rdfs:label "oral mucosa squamous cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral cortex glial cell) @@ -19746,6 +19397,8 @@ AnnotationAssertion(Annotation( "CALOHA:TS-1256") "cerebrum cortex glial cell") AnnotationAssertion(rdfs:label "cerebral cortex glial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral cortex endothelial cell) @@ -19756,6 +19409,9 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "cerebral cortex endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle fibroblast) @@ -19764,6 +19420,8 @@ AnnotationAssertion(Annotation( "CALOHA:TS-0643") AnnotationAssertion(rdfs:label "muscle fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone marrow hematopoietic cell) @@ -19773,6 +19431,8 @@ AnnotationAssertion(Annotation( "CALOHA:TS-2109") "bone marrow poietic cells") AnnotationAssertion(rdfs:label "bone marrow hematopoietic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (peripheral blood mononuclear cell) @@ -19784,6 +19444,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peripheral blood mononuclear cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain macroglial cell) @@ -19793,6 +19456,8 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000005") AnnotationAssertion(rdfs:label "brain macroglial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (microvascular endothelial cell) @@ -19802,6 +19467,8 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000008") AnnotationAssertion(rdfs:label "microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (dermis blood vessel endothelial cell) @@ -19811,6 +19478,8 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000010") AnnotationAssertion(rdfs:label "dermis blood vessel endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of skin of abdomen) @@ -19820,6 +19489,8 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000013") AnnotationAssertion(rdfs:label "fibroblast of skin of abdomen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung microvascular endothelial cell) @@ -19830,6 +19501,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (compound eye photoreceptor cell) @@ -19837,10 +19509,12 @@ SubClassOf( "GOC:TermGenie") "Any photoreceptor cell that is part of a compound eye.") AnnotationAssertion( ) AnnotationAssertion( "2014-06-24T23:16:45Z") -AnnotationAssertion( "FBbt:00004211") +AnnotationAssertion(Annotation( ) "FBbt:00006009") AnnotationAssertion( "CL:2000019") AnnotationAssertion(rdfs:label "compound eye photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (inner cell mass cell) @@ -19850,6 +19524,8 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000020") AnnotationAssertion(rdfs:label "inner cell mass cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac septum cell) @@ -19859,6 +19535,8 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000022") AnnotationAssertion(rdfs:label "cardiac septum cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord oligodendrocyte) @@ -19868,6 +19546,8 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000025") AnnotationAssertion(rdfs:label "spinal cord oligodendrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (central nervous system neuron) @@ -19877,10 +19557,13 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000029") AnnotationAssertion(rdfs:label "central nervous system neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (peripheral nervous system neuron) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "ISBN:0721662544") "A neuron that is part of a peripheral nervous system.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2014-06-25T02:28:17Z") AnnotationAssertion( "FMA:84664") @@ -19888,8 +19571,11 @@ AnnotationAssertion( "peripheral neuron") AnnotationAssertion( "CL:2000032") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peripheral nervous system neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic fibroblast) @@ -19900,6 +19586,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryonic fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain microvascular endothelial cell) @@ -19909,6 +19597,9 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000044") AnnotationAssertion(rdfs:label "brain microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ventricular cardiac muscle cell) @@ -19919,6 +19610,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ventricular cardiac muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brainstem motor neuron) @@ -19928,6 +19621,9 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000047") AnnotationAssertion(rdfs:label "brainstem motor neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian fibroblast) @@ -19938,6 +19634,8 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=7330") AnnotationAssertion(rdfs:label "ovarian fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian surface epithelial cell) @@ -19949,6 +19647,8 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=7310") AnnotationAssertion(rdfs:label "ovarian surface epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac ventricle fibroblast) @@ -19961,6 +19661,8 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=6310") AnnotationAssertion(rdfs:label "cardiac ventricle fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac atrium fibroblast) @@ -19973,6 +19675,8 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=6320") AnnotationAssertion(rdfs:label "cardiac atrium fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pericardium fibroblast) @@ -19983,6 +19687,8 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=6430") AnnotationAssertion(rdfs:label "pericardium fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (optic choroid fibroblast) @@ -19993,6 +19699,8 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=6620") AnnotationAssertion(rdfs:label "optic choroid fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (adipose microvascular endothelial cell) @@ -20003,6 +19711,9 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=7200") AnnotationAssertion(rdfs:label "adipose microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (migratory cardiac neural crest cell) @@ -20013,6 +19724,8 @@ AnnotationAssertion(Annotation( "CL:2000073") AnnotationAssertion(rdfs:label "migratory cardiac neural crest cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchymal stem cell of abdominal adipose tissue) @@ -20023,6 +19736,8 @@ AnnotationAssertion( "CL:2000080") AnnotationAssertion(rdfs:label "mesenchymal stem cell of abdominal adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (ciliated epithelial cell of esophagus) @@ -20032,6 +19747,9 @@ AnnotationAssertion( AnnotationAssertion( "CL:3000000") AnnotationAssertion(rdfs:label "ciliated epithelial cell of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (peripheral sensory neuron) @@ -20041,6 +19759,8 @@ AnnotationAssertion( AnnotationAssertion( "CL:3000004") AnnotationAssertion(rdfs:label "peripheral sensory neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (horizontal pyramidal neuron) @@ -20049,6 +19769,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "horizontal pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain vascular cell) @@ -20058,6 +19781,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain vascular cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (bitufted neuron) @@ -20067,6 +19792,8 @@ AnnotationAssertion(Annotation( "Int AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bitufted neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain-derived inhibitory neuron) @@ -20076,6 +19803,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "midbrain-derived inhibitory neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (inverted pyramidal neuron) @@ -20084,6 +19814,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "inverted pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (stellate pyramidal neuron) @@ -20092,6 +19825,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stellate pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (tufted pyramidal neuron) @@ -20100,6 +19836,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tufted pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (untufted pyramidal neuron) @@ -20108,6 +19847,9 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "untufted pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral cortex pyramidal neuron) @@ -20115,6 +19857,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "cerebral cortex pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (myelinating glial cell) @@ -20122,6 +19866,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "myelinating glial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (double bouquet cell) @@ -20129,6 +19875,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "double bouquet cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatosensory neuron) @@ -20136,6 +19884,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "somatosensory neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary capillary endothelial cell) @@ -20145,6 +19895,7 @@ AnnotationAssertion( AnnotationAssertion( "lung capillary endothelial cell") AnnotationAssertion(rdfs:label "pulmonary capillary endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20155,6 +19906,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood lymphocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) # Class: (respiratory ciliated cell) @@ -20163,7 +19916,8 @@ AnnotationAssertion( "ciliated cell of the respiratory tract") AnnotationAssertion(rdfs:label "respiratory ciliated cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vein endothelial cell of respiratory system) @@ -20173,6 +19927,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vein endothelial cell of respiratory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung megakaryocyte) @@ -20189,6 +19945,8 @@ AnnotationAssertion( "lung megakaryocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (taste receptor cell of tongue) @@ -20198,6 +19956,10 @@ AnnotationAssertion( "DOI:10.1016/s0022-5320(69)80043-2") "gustatory cell of tongue") AnnotationAssertion(rdfs:label "taste receptor cell of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (catecholaminergic neuron) @@ -20207,6 +19969,9 @@ AnnotationAssertion( "PMID:10191060") Annotation( "PMID:12128258") Annotation( "PMID:34880760") Annotation( "https://orcid.org/0000-0002-2244-7917") rdfs:comment "Frequently used when describing the developing nervous system in zebrafish. A catecholaminergic neuron expresses tyrosine hydroxylase (TH), tyrosine hydroxylase 2 (TH2), aromatic amino acid decarboxylase (AADC), dopamine b-hydroxylase (DBH), and phenylethanolamine-N-methyl transferase (PEMT), which are enzymes necessary for catecholamine synthesis.") AnnotationAssertion(rdfs:label "catecholaminergic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (perivascular cell) @@ -20215,6 +19980,8 @@ AnnotationAssertion( "2023-08-22T13:40:28Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "perivascular cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchymal stem cell of orbital adipose tissue) @@ -20226,23 +19993,8 @@ AnnotationAssertion(Annotation( "PMID:31377878") "orbital adipose-derived mesenchymal stem cell") AnnotationAssertion(rdfs:label "mesenchymal stem cell of orbital adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (reproduction) - -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:isa_complete") Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.") -AnnotationAssertion( "GO:0019952") -AnnotationAssertion( "GO:0050876") -AnnotationAssertion( "Wikipedia:Reproduction") -AnnotationAssertion( "reproductive physiological process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0000003") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "reproduction") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vacuole inheritance) @@ -20454,7 +20206,7 @@ AnnotationAssertion( "response to acid anion") AnnotationAssertion( "response to oxoanion") AnnotationAssertion( "GO:0001101") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. 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. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead.") AnnotationAssertion(rdfs:label "response to acid chemical") SubClassOf( ) @@ -20516,7 +20268,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "ciliary or bacterial-type flagellar motility") AnnotationAssertion( "GO:0001539") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent, while the bacterial- and archaeal-type flagella have a different structure. The former are microtubule-based structures that lash back and forth and are present only in eukaryotes, while the latter achieve motility by rotation. Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. These three structures never co-exist in the same organism. Therefore, GO:0001539 'cilium or flagellum-dependent cell motility' is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term. Direct annotations to GO:0001539 'cilium or flagellum-dependent cell motility' may be amended during annotation QC.") AnnotationAssertion(rdfs:label "cilium or flagellum-dependent cell motility") SubClassOf( ) @@ -20558,6 +20310,23 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (regulation of cell growth by extracellular stimulus) + +AnnotationAssertion(Annotation( "GOC:dph") "Any process in which external signals modulate the frequency, rate or extent of cell growth, the irreversible increase in size of a cell over time.") +AnnotationAssertion( "interpretation of external signals that regulate cell growth") +AnnotationAssertion( "regulation of cell growth by detection of exogenous stimulus") +AnnotationAssertion( "regulation of cell growth by sensing of exogenous stimulus") +AnnotationAssertion( "regulation of growth by exogenous signal") +AnnotationAssertion( "regulation of growth by exogenous stimuli") +AnnotationAssertion( "regulation of growth by exogenous stimulus") +AnnotationAssertion( "regulation of growth by external signal") +AnnotationAssertion( "regulation of growth by external stimuli") +AnnotationAssertion( "regulation of growth by external stimulus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0001560") +AnnotationAssertion(rdfs:label "regulation of cell growth by extracellular stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (blood vessel development) AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "UBERON:0001981") "The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.") @@ -21956,7 +21725,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0002790") AnnotationAssertion(rdfs:label "peptide secretion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -22004,7 +21773,7 @@ SubClassOf( "GOC:add") "Any process that modulates the frequency, rate, or extent of a response to biotic stimulus.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002831") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of response to biotic stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -22018,7 +21787,7 @@ AnnotationAssertion( "inhibition of response to biotic stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002832") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of response to biotic stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -22033,7 +21802,7 @@ AnnotationAssertion( "stimulation of response to biotic stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002833") -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 "positive regulation of response to biotic stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -22100,7 +21869,7 @@ AnnotationAssertion( "GOC:dph") Annotation( "GOC:tb") "reproductive developmental process") AnnotationAssertion( "GO:0003006") AnnotationAssertion(rdfs:label "developmental process involved in reproduction") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( )) SubClassOf( ) SubClassOf( ) @@ -23056,7 +22825,7 @@ AnnotationAssertion( "GO:0003333") AnnotationAssertion(rdfs:comment "Note that this term is not intended for use in annotating lateral movement within membranes.") AnnotationAssertion(rdfs:label "amino acid transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (cilium movement) @@ -23403,42 +23172,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (molecular_function) - -AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") -AnnotationAssertion( "GO:0005554") -AnnotationAssertion( "molecular function") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0003674") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") -AnnotationAssertion(rdfs:label "molecular_function") -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (catalytic activity) - -AnnotationAssertion(Annotation( "GOC:vw") Annotation( "ISBN:0198506732") "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.") -AnnotationAssertion( "Wikipedia:Enzyme") -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "enzyme activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0003824") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "catalytic activity") -SubClassOf( ) - # Class: (cellular_component) AnnotationAssertion(Annotation( "GOC:pdt") "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).") @@ -23471,13 +23204,16 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.") AnnotationAssertion(rdfs:label "extracellular region") @@ -23558,7 +23294,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term.") AnnotationAssertion(rdfs:label "extracellular space") SubClassOf( ) @@ -23597,12 +23332,14 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleus") SubClassOf( ) @@ -23660,6 +23397,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.") AnnotationAssertion(rdfs:label "chromosome") @@ -23697,7 +23435,9 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cytoplasm") SubClassOf( ) @@ -23714,11 +23454,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vacuole") SubClassOf( ) @@ -23757,10 +23499,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.") AnnotationAssertion(rdfs:label "Golgi apparatus") @@ -23792,6 +23536,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -23815,11 +23560,14 @@ AnnotationAssertion( "GO:0005840") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ribosome") SubClassOf( ) @@ -23837,11 +23585,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cytoskeleton") @@ -23931,11 +23681,14 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "plasma membrane") SubClassOf( ) @@ -24059,6 +23812,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -24161,7 +23915,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleobase-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) # Class: (DNA metabolic process) @@ -24179,9 +23932,10 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "DNA metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (chromatin organization) @@ -24266,12 +24020,14 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "translation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -24374,7 +24130,7 @@ AnnotationAssertion( "GO:0006518") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peptide metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (amino acid metabolic process) @@ -24393,6 +24149,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -24480,13 +24237,16 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lipid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -24511,19 +24271,6 @@ SubClassOf( ) SubClassOf( ) -# Class: (cellular aromatic compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.") -AnnotationAssertion( "aromatic compound metabolism") -AnnotationAssertion( "aromatic hydrocarbon metabolic process") -AnnotationAssertion( "aromatic hydrocarbon metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006725") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular aromatic compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (sulfur compound metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.") @@ -24543,40 +24290,6 @@ AnnotationAssertion(rdfs:label "sulf EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (phosphorus metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).") -AnnotationAssertion( "phosphorus metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006793") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphorus metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (phosphate-containing compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.") -AnnotationAssertion( "phosphate metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "phosphate metabolic process") -AnnotationAssertion( "GO:0006796") -AnnotationAssertion(rdfs:label "phosphate-containing compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (nitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "nitrogen compound metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006807") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "nitrogen compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (transport) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:mah") "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.") @@ -24595,7 +24308,9 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that 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, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.") AnnotationAssertion(rdfs:label "transport") SubClassOf( ) @@ -24612,29 +24327,6 @@ AnnotationAssertion( "monoatomic ion transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (monoatomic cation transport) - -AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom.") -AnnotationAssertion( "GO:0006819") -AnnotationAssertion( "GO:0015674") -AnnotationAssertion( "GO:0072512") -AnnotationAssertion( "cation transport") -AnnotationAssertion(Annotation( "GOC:mah") "di-, tri-valent inorganic cation transport") -AnnotationAssertion( "trivalent inorganic cation transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006812") -AnnotationAssertion(rdfs:label "monoatomic cation transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (phosphate ion transport) - -AnnotationAssertion(Annotation( "GOC:krc") "The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "phosphate transport") -AnnotationAssertion( "GO:0006817") -AnnotationAssertion(rdfs:label "phosphate ion transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (neurotransmitter transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.") @@ -24697,7 +24389,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino acid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (lipid transport) @@ -24711,28 +24403,6 @@ AnnotationAssertion(rdfs:label "lipi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (intracellular monoatomic ion homeostasis) - -AnnotationAssertion(Annotation( "GOC:mah") "A homeostatic process involved in the maintenance of a steady state level of monoatomic ions within a cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) -AnnotationAssertion( "cellular ion homeostasis") -AnnotationAssertion( "cellular monoatomic ion homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006873") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "intracellular monoatomic ion homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (regulation of pH) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:go_curators") Annotation( "GOC:tb") "Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell.") -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "hydrogen ion homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006885") -AnnotationAssertion(rdfs:label "regulation of pH") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (intracellular protein transport) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.") @@ -24958,12 +24628,12 @@ AnnotationAssertion( "response to abiotic stress") AnnotationAssertion( "response to biotic stress") AnnotationAssertion( "GO:0006950") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) 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( ) @@ -24998,6 +24668,7 @@ SubClassOf( ObjectAllValuesFrom( (organelle 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 an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-19T15:25:51Z") AnnotationAssertion( "GO:1902589") @@ -25007,8 +24678,10 @@ AnnotationAssertion( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:mah") "organelle organization and biogenesis") AnnotationAssertion( "single-organism organelle organization") AnnotationAssertion( "GO:0006996") +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 "organelle organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -25233,13 +24906,14 @@ AnnotationAssertion( "cell-division cycle") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0007049") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell cycle") SubClassOf( ) @@ -25379,20 +25053,17 @@ AnnotationAssertion( "GO:0023033") AnnotationAssertion( "GO:0023045") AnnotationAssertion( "Wikipedia:Signal_transduction") -AnnotationAssertion( "signal transduction by cis-phosphorylation") -AnnotationAssertion( "signal transduction by conformational transition") -AnnotationAssertion( "signal transduction by protein phosphorylation") -AnnotationAssertion( "signal transduction by trans-phosphorylation") AnnotationAssertion( "signaling cascade") AnnotationAssertion( "signalling cascade") AnnotationAssertion( "biological_process") AnnotationAssertion( "signaling pathway") -AnnotationAssertion(Annotation( "GOC:mah") "signalling pathway") +AnnotationAssertion( "signalling pathway") AnnotationAssertion( "GO:0007165") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.") AnnotationAssertion(rdfs:label "signal transduction") SubClassOf( ) @@ -25811,6 +25482,7 @@ SubClassOf( ObjectSomeValuesFrom( (heart development) AnnotationAssertion(Annotation( "GOC:jid") Annotation( "UBERON:0000948") "The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.") +AnnotationAssertion( ) AnnotationAssertion( "GO:0007511") AnnotationAssertion( "Wikipedia:Heart_development") AnnotationAssertion( "dorsal vessel development") @@ -25969,7 +25641,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism behavior") AnnotationAssertion( "GO:0007610") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "1. 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 reviews. @@ -26118,6 +25790,7 @@ SubClassOf( (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( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-17T15:46:40Z") AnnotationAssertion( "GO:0044236") @@ -26130,11 +25803,13 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism metabolic process") AnnotationAssertion( "GO:0008152") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +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( ) @@ -26273,6 +25948,7 @@ SubClassOf( ObjectAllValuesFrom( "GOC:bf") Annotation( "GOC:jl") "The orderly movement of a cell specialized to produce haploid gametes through the embryo from its site of production to the place where the gonads will form.") AnnotationAssertion( "germ-cell migration") +AnnotationAssertion( "pole cell migration") AnnotationAssertion( "biological_process") AnnotationAssertion( "primordial germ cell migration") AnnotationAssertion( "GO:0008354") @@ -26394,6 +26070,7 @@ SubClassOf( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17904"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27304"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Amino_acid_synthesis") AnnotationAssertion( "amino acid anabolism") AnnotationAssertion( "amino acid biosynthesis") @@ -26403,7 +26080,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0008652") AnnotationAssertion(rdfs:label "amino acid biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (biosynthetic process) @@ -26424,6 +26101,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "biosynthetic process") SubClassOf( ) @@ -26432,6 +26110,7 @@ SubClassOf( "GOC:mah") "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15249"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25418"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "GO:0043284") AnnotationAssertion(Annotation( "GOC:mtg_chebi_dec09") "biopolymer biosynthetic process") AnnotationAssertion( "macromolecule anabolism") @@ -26440,7 +26119,9 @@ AnnotationAssertion( "macromolecule synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009059") +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 "macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -26521,7 +26202,7 @@ AnnotationAssertion( "GO:0009309") AnnotationAssertion(rdfs:label "amine biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) # Class: (response to radiation) @@ -26617,7 +26298,7 @@ AnnotationAssertion(Annotation( "response to environmental stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009605") -AnnotationAssertion( ) +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.") @@ -26630,7 +26311,7 @@ AnnotationAssertion(Annotation( "response to biotic stress") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009607") -AnnotationAssertion( ) +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.") @@ -26667,7 +26348,7 @@ AnnotationAssertion( "response to abiotic stress") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009628") -AnnotationAssertion( ) +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.") @@ -26730,7 +26411,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:sm") "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 arising within the organism.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009719") -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 endogenous stimulus") @@ -26739,6 +26420,8 @@ SubClassOf( (response to hormone) AnnotationAssertion(Annotation( "GOC:jl") "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 hormone stimulus.") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(Annotation( "GOC:dos") "response to hormone stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "growth regulator") @@ -26746,6 +26429,12 @@ AnnotationAssertion( "response to hormone") SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (response to carbohydrate) @@ -26774,7 +26463,7 @@ AnnotationAssertion( "embryonal development") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009790") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryo development") @@ -26851,6 +26540,8 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (tissue development) @@ -27129,10 +26820,13 @@ SubClassOf( (response to organic substance) AnnotationAssertion(Annotation( "GOC:sm") Annotation( "PMID:23356676") "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 organic substance stimulus.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "GO:1990367") AnnotationAssertion( "process resulting in tolerance to organic substance") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010033") +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 organic substance") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -27188,9 +26882,12 @@ SubClassOf( (response to organonitrogen compound) AnnotationAssertion(Annotation( "PMID:9869419") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "response to organic nitrogen") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010243") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "response to organonitrogen compound") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -27273,6 +26970,8 @@ AnnotationAssertion( "GOC:cjm") "gene regulation") AnnotationAssertion( "regulation of gene product expression") AnnotationAssertion( "GO:0010468") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.") AnnotationAssertion(rdfs:label "regulation of gene expression") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -27384,22 +27083,6 @@ AnnotationAssertion( "negative regulation of glycoprotein biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (positive regulation of phosphorus metabolic process) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010562") -AnnotationAssertion(rdfs:label "positive regulation of phosphorus metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of phosphorus metabolic process) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010563") -AnnotationAssertion(rdfs:label "negative regulation of phosphorus metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of cell cycle process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.") @@ -28106,16 +27789,6 @@ AnnotationAssertion( "regulation of amino acid import across plasma membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of phosphate transport) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of phosphate transport. Phosphate transport is the directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "tb") -AnnotationAssertion( "2009-05-20T11:42:50Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010966") -AnnotationAssertion(rdfs:label "regulation of phosphate transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of microtubule nucleation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell.") @@ -28203,9 +27876,11 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "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") @@ -29013,7 +28688,7 @@ AnnotationAssertion( "GO:0015833") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peptide transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -29151,10 +28826,12 @@ AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mah") "cell organization and biogenesis") AnnotationAssertion( "GO:0016043") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -29243,6 +28920,7 @@ AnnotationAssertion( "GO:0016070") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -29264,6 +28942,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -29280,35 +28959,6 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) 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( "molecular_function") -AnnotationAssertion( "GO:0016301") -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( ) -SubClassOf( ObjectHasSelf()) - -# 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( "Wikipedia:Phosphorylation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0016310") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "phosphorylation") -SubClassOf( ) - # Class: (female meiosis chromosome segregation) AnnotationAssertion(Annotation( "GOC:ai") "The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female.") @@ -29398,40 +29048,6 @@ SubClassOf( ObjectComplementOf(Object SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (transferase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") -AnnotationAssertion( "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") -AnnotationAssertion(Annotation(rdfs:label "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK") "Reactome:R-HSA-5668414") -AnnotationAssertion(Annotation(rdfs:label "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248") "Reactome:R-HSA-8868783") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016740") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "transferase activity") -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( "molecular_function") -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: (response to insecticide) AnnotationAssertion(Annotation( "GOC:curators") "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 insecticide stimulus. Insecticides are chemicals used to kill insects.") @@ -29493,20 +29109,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (heterocycle biosynthetic process) - -AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).") -AnnotationAssertion( "heterocycle anabolism") -AnnotationAssertion( "heterocycle biosynthesis") -AnnotationAssertion( "heterocycle formation") -AnnotationAssertion( "heterocycle synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0018130") -AnnotationAssertion(rdfs:label "heterocycle biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (phenol-containing compound metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring.") @@ -29521,7 +29123,6 @@ AnnotationAssertion( "Note that phenol metabolism is not included as a child of 'xenobiotic metabolism' because although it is synthesized industrially, phenol is also found naturally in animal wastes and other organic materials. It is often formed by the activity of microorganisms, which can chemically modify a variety of xenobiotic and naturally occurring phenolic compounds.") AnnotationAssertion(rdfs:label "phenol-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -29542,7 +29143,7 @@ AnnotationAssertion( "single-organism reproductive behavior") AnnotationAssertion( "GO:0019098") AnnotationAssertion(rdfs:label "reproductive behavior") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( )) # Class: (regulation of lipid metabolic process) @@ -29574,15 +29175,6 @@ AnnotationAssertion( "regulation of nucleobase-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of phosphate metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.") -AnnotationAssertion( "regulation of phosphate metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0019220") -AnnotationAssertion(rdfs:label "regulation of phosphate metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.") @@ -29643,26 +29235,11 @@ AnnotationAssertion( "acetate biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (aromatic compound biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.") -AnnotationAssertion( "aromatic compound anabolism") -AnnotationAssertion( "aromatic compound biosynthesis") -AnnotationAssertion( "aromatic compound formation") -AnnotationAssertion( "aromatic compound synthesis") -AnnotationAssertion( "aromatic hydrocarbon biosynthesis") -AnnotationAssertion( "aromatic hydrocarbon biosynthetic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0019438") -AnnotationAssertion(rdfs:label "aromatic compound biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (protein metabolic process) AnnotationAssertion(Annotation( "GOC:ma") "The chemical reactions and pathways involving a protein. Includes protein modification.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "GO:0006411") AnnotationAssertion( "GO:0044267") AnnotationAssertion( "GO:0044268") @@ -29675,11 +29252,14 @@ AnnotationAssertion( "multicellular organismal protein metabolic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019538") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) 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 "protein metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -29690,6 +29270,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0019725") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular homeostasis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -29707,8 +29288,10 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019748") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "secondary metabolic process") SubClassOf( ) @@ -29751,7 +29334,7 @@ AnnotationAssertion( "GO:0019953") AnnotationAssertion(rdfs:comment "Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.") AnnotationAssertion(rdfs:label "sexual reproduction") -SubClassOf( ) +SubClassOf( ) # Class: (prechordal plate formation) @@ -30988,6 +30571,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0022402") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell cycle process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -31003,12 +30587,15 @@ SubClassOf( (cellular component disassembly) AnnotationAssertion(Annotation( "GOC:isa_complete") "A cellular process that results in the breakdown of a cellular component.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "GO:0071845") AnnotationAssertion( "cell structure disassembly") AnnotationAssertion( "cellular component disassembly at cellular level") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022411") +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 "cellular component disassembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -31022,22 +30609,30 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022412") AnnotationAssertion(rdfs:label "cellular process involved in reproduction in multicellular organism") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( )) SubClassOf( ) -SubClassOf( ) # Class: (reproductive process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:isa_complete") "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:56:06Z") AnnotationAssertion( "GO:0044702") +AnnotationAssertion( "Wikipedia:Reproduction") AnnotationAssertion( "biological_process") AnnotationAssertion( "single organism reproductive process") AnnotationAssertion( "GO:0022414") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reproductive process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (digestive system process) @@ -31079,6 +30674,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022607") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -31181,11 +30777,13 @@ AnnotationAssertion(Annotation( "single organism signaling") AnnotationAssertion( "GO:0023052") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.") AnnotationAssertion(rdfs:label "signaling") @@ -31230,17 +30828,6 @@ AnnotationAssertion(rdfs:label "sign EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (intracellular monoatomic cation homeostasis) - -AnnotationAssertion(Annotation( "GOC:ceb") Annotation( "GOC:mah") "A homeostatic process involved in the maintenance of a steady state level of monoatomic cations within a cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) -AnnotationAssertion( "cellular cation homeostasis") -AnnotationAssertion( "cellular monoatomic cation homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0030003") -AnnotationAssertion(rdfs:label "intracellular monoatomic cation homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (establishment of cell polarity) AnnotationAssertion(Annotation( "GOC:mah") "The specification and formation of anisotropic intracellular organization or cell growth patterns.") @@ -31382,6 +30969,8 @@ AnnotationAssertion( "GO:0030097") AnnotationAssertion(rdfs:label "hemopoiesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (lymphocyte differentiation) @@ -31452,6 +31041,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -31804,30 +31394,6 @@ AnnotationAssertion( "smooth muscle contractile fiber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (intracellular sulfate ion homeostasis) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:24193406") "A homeostatic process involved in the maintenance of a steady state level of sulfate ions within a cell.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24514"^^xsd:anyURI) -AnnotationAssertion( "sulphate ion homeostasis") -AnnotationAssertion( "cellular sulfate ion homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0030642") -AnnotationAssertion(rdfs:label "intracellular sulfate ion homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (intracellular phosphate ion homeostasis) - -AnnotationAssertion(Annotation( "GOC:mah") "A homeostatic process involved in the maintenance of a steady state level of phosphate ions within a cell.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26429"^^xsd:anyURI) -AnnotationAssertion( "intracellular phosphate homeostasis") -AnnotationAssertion( "cellular phosphate ion homeostasis") -AnnotationAssertion( "intracellular Pi homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0030643") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "intracellular phosphate ion homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (transport vesicle membrane) AnnotationAssertion(Annotation( "GOC:mah") "The lipid bilayer surrounding a transport vesicle.") @@ -32066,6 +31632,7 @@ AnnotationAssertion( "GO:0031012") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -32303,10 +31870,12 @@ SubClassOf( ObjectSomeValuesFrom( (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( "biological_process") 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( ) @@ -32315,6 +31884,7 @@ SubClassOf( (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") @@ -32323,6 +31893,7 @@ AnnotationAssertion( "biological_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( ) @@ -32332,6 +31903,7 @@ SubClassOf( (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") @@ -32341,6 +31913,7 @@ AnnotationAssertion( "biological_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( ) @@ -32350,12 +31923,15 @@ SubClassOf( (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( "biological_process") 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( ) @@ -32364,6 +31940,7 @@ SubClassOf( (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") @@ -32374,6 +31951,8 @@ AnnotationAssertion( "inhibition of cellular biosynthetic process") AnnotationAssertion( "biological_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( ) @@ -32383,6 +31962,7 @@ SubClassOf( (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") @@ -32394,6 +31974,8 @@ AnnotationAssertion( "stimulation of cellular biosynthetic process") AnnotationAssertion( "biological_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( ) @@ -32567,15 +32149,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of buoyancy) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PATO:0001420") "Any process that modulates an organism's tendency or ability to rise or float in a fluid medium such as water or air, often through the use of stored gases.") -AnnotationAssertion( "buoyancy regulation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031413") -AnnotationAssertion(rdfs:label "regulation of buoyancy") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (protein-containing complex localization) AnnotationAssertion(Annotation( "GOC:mah") "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.") @@ -32659,6 +32232,8 @@ AnnotationAssertion( "positive regulation of myelination") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (regulation of nervous system process) @@ -32722,7 +32297,7 @@ AnnotationAssertion( "GO:0031967") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle envelope") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -32746,15 +32321,6 @@ AnnotationAssertion(rdfs:label "memb SubClassOf( ) DisjointClasses( ) -# Class: (envelope) - -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:pz") "A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0031975") -AnnotationAssertion(rdfs:label "envelope") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (nuclear lumen) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:pz") "The volume enclosed by the nuclear inner membrane.") @@ -32841,7 +32407,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of a response to an external stimulus.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032101") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of response to external stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -32856,7 +32422,7 @@ AnnotationAssertion( "inhibition of response to external stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032102") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of response to external stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -32873,7 +32439,7 @@ AnnotationAssertion( "stimulation of response to external stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032103") -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 "positive regulation of response to external stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -33116,17 +32682,6 @@ SubClassOf( ) SubClassOf( ) -# Class: (intracellular oxygen homeostasis) - -AnnotationAssertion(Annotation( "GOC:rph") "A homeostatic process involved in the maintenance of a steady state level of oxygen within a cell.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24224"^^xsd:anyURI) -AnnotationAssertion( "oxygen homeostasis") -AnnotationAssertion( "cellular oxygen homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032364") -AnnotationAssertion(rdfs:label "intracellular oxygen homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (intracellular lipid transport) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of lipids within cells.") @@ -33245,6 +32800,7 @@ EquivalentClasses( ObjectIntersection # Class: (multicellular organismal process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -33259,6 +32815,7 @@ AnnotationAssertion( "GO:0032501") 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 "multicellular organismal process") SubClassOf( ) SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) @@ -33290,16 +32847,6 @@ AnnotationAssertion( "developmental process") SubClassOf( ) -# Class: (multicellular organism reproduction) - -AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:jid") "The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032504") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "multicellular organism reproduction") -SubClassOf( ) -SubClassOf( ) - # Class: (maintenance of protein location in cell) AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:mah") "Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.") @@ -33435,9 +32982,11 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of localization) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:mah") "regulation of localisation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032879") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of localization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -33675,7 +33224,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032973") AnnotationAssertion(rdfs:label "amino acid export across plasma membrane") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (amino acid transmembrane export from vacuole) @@ -33685,7 +33234,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032974") AnnotationAssertion(rdfs:label "amino acid transmembrane export from vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (amino acid transmembrane import into vacuole) @@ -33694,7 +33243,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032975") AnnotationAssertion(rdfs:label "amino acid transmembrane import into vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (protein-containing complex disassembly) @@ -33747,7 +33296,7 @@ AnnotationAssertion( "GO:0032989") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular anatomical entity morphogenesis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (protein-containing complex) @@ -33762,6 +33311,7 @@ AnnotationAssertion( "GO:0032991") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -34007,14 +33557,6 @@ AnnotationAssertion( "protein localization to secretory granule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (carbohydrate homeostasis) - -AnnotationAssertion(Annotation( "GOC:mah") "A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0033500") -AnnotationAssertion(rdfs:label "carbohydrate homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (negative regulation of catecholamine secretion) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine.") @@ -34046,36 +33588,6 @@ SubClassOf( ) SubClassOf( ) -# 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( "biological_process") -AnnotationAssertion( "GO:0033673") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of kinase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") 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( "biological_process") -AnnotationAssertion( "GO:0033674") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of kinase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) - # Class: (ribosome localization) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a ribosome is transported to, and/or maintained in, a specific location.") @@ -34355,7 +33867,7 @@ AnnotationAssertion( "GO:0034487") AnnotationAssertion(rdfs:comment "Note that this term is not intended for use in annotating lateral movement within membranes.") AnnotationAssertion(rdfs:label "vacuolar amino acid transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (protein localization to chromosome) @@ -34381,19 +33893,6 @@ AnnotationAssertion( "protein localization to nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (cellular nitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "cellular nitrogen compound metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0034641") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular nitrogen compound metabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (nucleobase-containing compound biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.") @@ -34405,7 +33904,6 @@ AnnotationAssertion( "GO:0034654") AnnotationAssertion(rdfs:label "nucleobase-containing compound biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (regulation of transmembrane transport) @@ -34740,18 +34238,6 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "acetate transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -# Class: (phosphate ion transmembrane transport) - -AnnotationAssertion(Annotation( "GOC:vw") "The process in which a phosphate is transported across a membrane.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2010-04-08T11:24:06Z") -AnnotationAssertion( "phosphate ion membrane transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0035435") -AnnotationAssertion(rdfs:comment "Note that this term is not intended for use in annotating lateral movement within membranes.") -AnnotationAssertion(rdfs:label "phosphate ion transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) - # Class: (cell migration involved in vasculogenesis) AnnotationAssertion(Annotation( "GOC:dgh") "The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form de novo blood vessels and tubes.") @@ -35572,11 +35058,12 @@ AnnotationAssertion(Annotation( "response to chemical substance") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042221") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) 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 chemical") @@ -35597,6 +35084,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ribosome biogenesis") SubClassOf( ) @@ -35655,39 +35143,6 @@ AnnotationAssertion( "negative regulation of protein import into nucleus") EquivalentClasses( ObjectIntersectionOf( 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( "biological_process") -AnnotationAssertion( "GO:0042325") -AnnotationAssertion(rdfs:label "regulation of phosphorylation") -EquivalentClasses( ObjectIntersectionOf( 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( "down regulation of phosphorylation") -AnnotationAssertion( "down-regulation of phosphorylation") -AnnotationAssertion( "downregulation of phosphorylation") -AnnotationAssertion( "inhibition of phosphorylation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0042326") -AnnotationAssertion(rdfs:label "negative regulation of phosphorylation") -EquivalentClasses( ObjectIntersectionOf( 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( "biological_process") -AnnotationAssertion( "GO:0042327") -AnnotationAssertion(rdfs:label "positive regulation of phosphorylation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of membrane potential) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mtg_cardio") Annotation( "GOC:tb") Annotation( "ISBN:0198506732") "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.") @@ -35794,9 +35249,6 @@ AnnotationAssertion( "GO:0042430") AnnotationAssertion(rdfs:label "indole-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -35813,12 +35265,8 @@ AnnotationAssertion( "GO:0042435") AnnotationAssertion(rdfs:label "indole-containing compound biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (photoreceptor cell development) @@ -35993,6 +35441,7 @@ SubClassOf( (regulation of apoptotic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mtg_apoptosis") "Any process that modulates the occurrence or rate of cell death by apoptotic process.") +AnnotationAssertion( ) AnnotationAssertion( "regulation of apoptosis") AnnotationAssertion( "biological_process") AnnotationAssertion( "apoptosis regulator activity") @@ -36000,6 +35449,9 @@ AnnotationAssertion( "This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.") AnnotationAssertion(rdfs:label "regulation of apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (cell projection) @@ -36010,10 +35462,12 @@ AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0042995") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell projection") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -36133,7 +35587,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043043") AnnotationAssertion(rdfs:label "peptide biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (extracellular structure organization) @@ -36167,6 +35621,7 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of apoptotic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.") +AnnotationAssertion( ) AnnotationAssertion( "GO:0006916") AnnotationAssertion( "anti-apoptosis") AnnotationAssertion( "down regulation of apoptosis") @@ -36181,6 +35636,9 @@ AnnotationAssertion( "This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.") AnnotationAssertion(rdfs:label "negative regulation of apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (regulation of programmed cell death) @@ -36231,49 +35689,6 @@ AnnotationAssertion(rdfs:label "germ EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (positive regulation of catalytic activity) - -AnnotationAssertion(Annotation( "GOC:ebc") Annotation( "GOC:jl") Annotation( "GOC:tb") Annotation( "GOC:vw") "Any process that activates or increases the activity of an enzyme.") -AnnotationAssertion( "GO:0048554") -AnnotationAssertion(Annotation( "GOC:tb") "positive regulation of enzyme activity") -AnnotationAssertion( "up regulation of enzyme activity") -AnnotationAssertion( "up-regulation of enzyme activity") -AnnotationAssertion( "upregulation of enzyme activity") -AnnotationAssertion( "activation of enzyme activity") -AnnotationAssertion( "activation of metalloenzyme activity") -AnnotationAssertion( "positive regulation of metalloenzyme activity") -AnnotationAssertion( "stimulation of enzyme activity") -AnnotationAssertion( "stimulation of metalloenzyme activity") -AnnotationAssertion( "up regulation of metalloenzyme activity") -AnnotationAssertion( "up-regulation of metalloenzyme activity") -AnnotationAssertion( "upregulation of metalloenzyme activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0043085") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of catalytic activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of catalytic activity) - -AnnotationAssertion(Annotation( "GOC:ebc") Annotation( "GOC:jl") Annotation( "GOC:tb") Annotation( "GOC:vw") "Any process that stops or reduces the activity of an enzyme.") -AnnotationAssertion( "GO:0048553") -AnnotationAssertion( "down regulation of enzyme activity") -AnnotationAssertion( "down-regulation of enzyme activity") -AnnotationAssertion( "down-regulation of metalloenzyme activity") -AnnotationAssertion( "downregulation of enzyme activity") -AnnotationAssertion(Annotation( "GOC:tb") "negative regulation of enzyme activity") -AnnotationAssertion( "down regulation of metalloenzyme activity") -AnnotationAssertion( "downregulation of metalloenzyme activity") -AnnotationAssertion( "inhibition of enzyme activity") -AnnotationAssertion( "inhibition of metalloenzyme activity") -AnnotationAssertion( "negative regulation of metalloenzyme activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0043086") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of catalytic activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of translation by machinery localization) AnnotationAssertion(Annotation( "GOC:jl") "Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location.") @@ -36335,7 +35750,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0043200") AnnotationAssertion(rdfs:label "response to amino acid") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (response to external biotic stimulus) @@ -36376,6 +35791,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle") SubClassOf( ) @@ -36580,17 +35996,20 @@ AnnotationAssertion( "response to alkaloid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (contractile fiber) +# Class: (contractile muscle fiber) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0815316194") "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27281"^^xsd:anyURI) AnnotationAssertion( "contractile fibre") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0043292") -AnnotationAssertion(rdfs:label "contractile fiber") +AnnotationAssertion(rdfs:label "contractile muscle fiber") SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (enucleate erythrocyte differentiation) @@ -36813,16 +36232,6 @@ AnnotationAssertion( "endothelial cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# 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( "biological_process") -AnnotationAssertion( "GO:0043549") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of kinase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) - # 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.") @@ -36886,11 +36295,14 @@ SubClassOf( ObjectSomeValuesFrom( (amide metabolic process) AnnotationAssertion(Annotation( "GOC:curators") "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "amide metabolism") AnnotationAssertion( "cellular amide metabolic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043603") +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 "amide metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -36902,7 +36314,6 @@ AnnotationAssertion( "amide biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (ossification involved in bone maturation) @@ -37031,30 +36442,6 @@ AnnotationAssertion( "membrane biogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (negative regulation of molecular function) - -AnnotationAssertion(Annotation( "GO:jl") "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2009-04-21T04:07:27Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044092") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negative regulation of molecular function") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (positive regulation of molecular function) - -AnnotationAssertion(Annotation( "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( "jl") -AnnotationAssertion( "2009-04-21T04:11:06Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044093") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positive regulation of molecular function") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (translation initiation ternary complex) AnnotationAssertion(Annotation( "GOC:jl") "A ribonucleoprotein complex that contains 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).") @@ -37089,36 +36476,29 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044238") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "primary metabolic process") 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( "biological_process") 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 nitrogen compound biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.") -AnnotationAssertion( "nitrogen compound anabolism") -AnnotationAssertion( "nitrogen compound biosynthesis") -AnnotationAssertion( "nitrogen compound formation") -AnnotationAssertion( "nitrogen compound synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044271") -AnnotationAssertion(rdfs:label "cellular nitrogen compound biosynthetic 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.") @@ -37158,6 +36538,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044283") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.") AnnotationAssertion(rdfs:label "small molecule biosynthetic process") SubClassOf( ) @@ -37446,6 +36827,7 @@ AnnotationAssertion(Annotation( "GO:0045202") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -38410,25 +37792,6 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (pH reduction) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that reduces the internal pH of an organism, part of an organism or a cell, measured by the concentration of the hydrogen ion.") -AnnotationAssertion( "acidification") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045851") -AnnotationAssertion(rdfs:label "pH reduction") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (pH elevation) - -AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that increases the internal pH of an organism, part of an organism or a cell, measured by the concentration of the hydrogen ion.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045852") -AnnotationAssertion(rdfs:label "pH elevation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (negative regulation of translational elongation) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.") @@ -38690,33 +38053,6 @@ AnnotationAssertion( "positive regulation of nucleobase-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (negative regulation of phosphate 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 phosphates.") -AnnotationAssertion( "down regulation of phosphate metabolic process") -AnnotationAssertion( "down-regulation of phosphate metabolic process") -AnnotationAssertion( "downregulation of phosphate metabolic process") -AnnotationAssertion( "negative regulation of phosphate metabolism") -AnnotationAssertion( "inhibition of phosphate metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045936") -AnnotationAssertion(rdfs:label "negative regulation of phosphate metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of phosphate 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 phosphates.") -AnnotationAssertion( "positive regulation of phosphate metabolism") -AnnotationAssertion( "up regulation of phosphate metabolic process") -AnnotationAssertion( "up-regulation of phosphate metabolic process") -AnnotationAssertion( "upregulation of phosphate metabolic process") -AnnotationAssertion( "activation of phosphate metabolic process") -AnnotationAssertion( "stimulation of phosphate metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0045937") -AnnotationAssertion(rdfs:label "positive regulation of phosphate metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (negative regulation of steroid 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 steroids.") @@ -38909,17 +38245,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (heterocycle metabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).") -AnnotationAssertion( "heterocycle metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0046483") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "heterocycle metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (photoreceptor cell differentiation) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "ISBN:0198506732") "The specialization of organization of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. An example of this process is found in Drosophila melanogaster.") @@ -40244,7 +39569,7 @@ SubClassOf( "GOC:jid") "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048583") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of response to stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -40260,7 +39585,7 @@ AnnotationAssertion( "stimulation of response to stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048584") -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 "positive regulation of response to stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -40276,7 +39601,7 @@ AnnotationAssertion( "inhibition of response to stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048585") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of response to stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -40389,13 +39714,15 @@ SubClassOf( ObjectSomeValuesFrom( (multicellular organismal reproductive process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") Annotation( "GOC:tb") "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) AnnotationAssertion( "organismal reproductive process") AnnotationAssertion( "reproductive process in a multicellular organism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048609") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "multicellular organismal reproductive process") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (myoblast development) @@ -41088,6 +40415,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anatomical structure development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -41166,6 +40494,7 @@ SubClassOf( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:mlg") "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19809"^^xsd:anyURI) +AnnotationAssertion( ) AnnotationAssertion( "cell locomotion") AnnotationAssertion( "movement of a cell") AnnotationAssertion( "biological_process") @@ -41173,10 +40502,14 @@ AnnotationAssertion( "GO:0048870") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell motility") SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (multicellular organismal-level homeostasis) @@ -41198,15 +40531,6 @@ AnnotationAssertion( "homeostasis of number of cells") SubClassOf( ) -# Class: (chemical homeostasis) - -AnnotationAssertion(Annotation( "GOC:isa_complete") "Any biological process involved in the maintenance of an internal steady state of a chemical.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0048878") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "chemical homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (sensory system development) AnnotationAssertion(Annotation( "GOC:dgh") "The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure.") @@ -41584,19 +40908,6 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (regulation of catalytic activity) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:ebc") Annotation( "GOC:vw") "Any process that modulates the activity of an enzyme.") -AnnotationAssertion( "GO:0048552") -AnnotationAssertion( "regulation of enzyme activity") -AnnotationAssertion( "regulation of metalloenzyme activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0050790") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of catalytic activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of developmental process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).") @@ -41627,20 +40938,6 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (monoatomic ion homeostasis) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process involved in the maintenance of an internal steady state of monoatomic ions within an organism or cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) -AnnotationAssertion( "GO:2000021") -AnnotationAssertion( "ion homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "electrolyte homeostasis") -AnnotationAssertion( "negative regulation of crystal formation") -AnnotationAssertion( "regulation of ion homeostasis") -AnnotationAssertion( "GO:0050801") -AnnotationAssertion(rdfs:label "monoatomic ion homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of synapse structure or activity) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).") @@ -41753,11 +41050,15 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell activation) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.") +AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050865") AnnotationAssertion(rdfs:label "regulation of cell activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (negative regulation of cell activation) @@ -41819,6 +41120,7 @@ SubClassOf( (musculoskeletal movement) AnnotationAssertion(Annotation( "GOC:dph") "The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system.") +AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050881") AnnotationAssertion(rdfs:label "musculoskeletal movement") @@ -41854,12 +41156,13 @@ AnnotationAssertion( "physiological response to stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050896") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) 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 stimulus") SubClassOf( ) @@ -42483,59 +41786,6 @@ AnnotationAssertion( "import into nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -# Class: (regulation of nitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") -AnnotationAssertion(Annotation( "GOC:tb") "regulation of nitrogen metabolic process") -AnnotationAssertion( "regulation of nitrogen metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051171") -AnnotationAssertion(rdfs:label "regulation of nitrogen compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (negative regulation of nitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") -AnnotationAssertion( "down regulation of nitrogen metabolic process") -AnnotationAssertion( "down-regulation of nitrogen metabolic process") -AnnotationAssertion( "downregulation of nitrogen metabolic process") -AnnotationAssertion(Annotation( "GOC:tb") "negative regulation of nitrogen metabolic process") -AnnotationAssertion( "negative regulation of nitrogen metabolism") -AnnotationAssertion( "inhibition of nitrogen metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051172") -AnnotationAssertion(rdfs:label "negative regulation of nitrogen compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - -# Class: (positive regulation of nitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") -AnnotationAssertion(Annotation( "GOC:tb") "positive regulation of nitrogen metabolic process") -AnnotationAssertion( "positive regulation of nitrogen metabolism") -AnnotationAssertion( "up regulation of nitrogen metabolic process") -AnnotationAssertion( "up-regulation of nitrogen metabolic process") -AnnotationAssertion( "upregulation of nitrogen metabolic process") -AnnotationAssertion( "activation of nitrogen metabolic process") -AnnotationAssertion( "stimulation of nitrogen metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051173") -AnnotationAssertion(rdfs:label "positive regulation of nitrogen compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - -# Class: (regulation of phosphorus metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.") -AnnotationAssertion( "regulation of phosphorus metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051174") -AnnotationAssertion(rdfs:label "regulation of phosphorus metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (negative regulation of sulfur metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur.") @@ -42570,6 +41820,7 @@ EquivalentClasses( ObjectIntersection # Class: (localization) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dos") "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27052"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-18T13:51:04Z") AnnotationAssertion( "GO:1902578") @@ -42583,6 +41834,7 @@ AnnotationAssertion( "GOC:TermGenie") "single organism localization") AnnotationAssertion( "single-organism localization") AnnotationAssertion( "GO:0051179") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "localization") SubClassOf( ) @@ -42956,51 +42208,6 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) -# Class: (regulation of transferase activity) - -AnnotationAssertion(Annotation( "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( "biological_process") -AnnotationAssertion( "GO:0051338") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") -AnnotationAssertion(rdfs:label "regulation of transferase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of transferase activity) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases 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 a donor compound to an acceptor.") -AnnotationAssertion( "transferase activator") -AnnotationAssertion( "up regulation of transferase activity") -AnnotationAssertion( "up-regulation of transferase activity") -AnnotationAssertion( "upregulation of transferase activity") -AnnotationAssertion( "activation of transferase activity") -AnnotationAssertion( "stimulation of transferase activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051347") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") -AnnotationAssertion(rdfs:label "positive regulation of transferase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of transferase activity) - -AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops or reduces the rate 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 a donor compound to an acceptor.") -AnnotationAssertion( "down regulation of transferase activity") -AnnotationAssertion( "down-regulation of transferase activity") -AnnotationAssertion( "downregulation of transferase activity") -AnnotationAssertion( "transferase inhibitor") -AnnotationAssertion( "inhibition of transferase activity") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051348") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") -AnnotationAssertion(rdfs:label "negative regulation of transferase activity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (neuron apoptotic process) AnnotationAssertion(Annotation( "CL:0000540") Annotation( "GOC:mtg_apoptosis") "Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.") @@ -43329,6 +42536,7 @@ SubClassOf( ObjectAllValuesFrom( (cellular localization) AnnotationAssertion(Annotation( "GOC:tb") Annotation( "GOC:vw") "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-18T14:04:32Z") AnnotationAssertion( "GO:1902580") @@ -43341,7 +42549,9 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism cellular localization") AnnotationAssertion( "GO:0051641") +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 "cellular localization") SubClassOf( ) SubClassOf( ) @@ -43551,7 +42761,7 @@ SubClassOf( "GOC:bf") Annotation( "GOC:jl") "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. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051716") -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 "cellular response to stimulus") SubClassOf( ) @@ -43825,6 +43035,8 @@ AnnotationAssertion( "regulation of nervous system development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (negative regulation of nervous system development) @@ -44239,48 +43451,6 @@ AnnotationAssertion(rdfs:label "asym EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (phosphate ion homeostasis) - -AnnotationAssertion(Annotation( "GOC:jid") Annotation( "GOC:mah") "Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26429"^^xsd:anyURI) -AnnotationAssertion( "phosphate homeostasis") -AnnotationAssertion( "Pi homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0055062") -AnnotationAssertion(rdfs:label "phosphate ion homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (sulfate ion homeostasis) - -AnnotationAssertion(Annotation( "GOC:jid") Annotation( "GOC:mah") "Any process involved in the maintenance of an internal steady state of sulfate ions within an organism or cell.") -AnnotationAssertion( "GO:0080174") -AnnotationAssertion( "sulfate homeostasis") -AnnotationAssertion( "sulphate ion homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0055063") -AnnotationAssertion(rdfs:label "sulfate ion homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (monoatomic cation homeostasis) - -AnnotationAssertion(Annotation( "GOC:ceb") Annotation( "GOC:jid") Annotation( "GOC:mah") "Any process involved in the maintenance of an internal steady state of monoatomic cations within an organism or cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) -AnnotationAssertion( "cation homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0055080") -AnnotationAssertion(rdfs:label "monoatomic cation homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (intracellular chemical homeostasis) - -AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:jid") "A homeostatic process involved in the maintenance of a steady state level of a chemical within a cell.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24514"^^xsd:anyURI) -AnnotationAssertion( "cellular chemical homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0055082") -AnnotationAssertion(rdfs:label "intracellular chemical homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (transmembrane transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.") @@ -44293,6 +43463,7 @@ AnnotationAssertion( "GO:0055085") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -44317,14 +43488,6 @@ AnnotationAssertion(rdfs:label "nucl SubClassOf( ) SubClassOf( ) -# Class: (lipid homeostasis) - -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:rl") "Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0055088") -AnnotationAssertion(rdfs:label "lipid homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (Golgi to secretory granule transport) AnnotationAssertion(Annotation( "GOC:curators") "The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bounded particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex.") @@ -44921,16 +44084,6 @@ AnnotationAssertion(rdfs:label "cran EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (regulation of brood size) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates brood size. Brood size is the number of progeny that survive embryogenesis and are cared for at one time.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0060378") -AnnotationAssertion(rdfs:label "regulation of brood size") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (cardiac muscle cell myoblast differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which a relatively unspecialized cell acquires specialized features of a cardiac myoblast. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life.") @@ -46185,6 +45338,8 @@ AnnotationAssertion( "GO:0060998") AnnotationAssertion(rdfs:label "regulation of dendritic spine development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) # Class: (positive regulation of dendritic spine development) @@ -47329,17 +46484,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (transferase complex, transferring phosphorus-containing groups) - -AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "GOC:dph") "A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") -AnnotationAssertion( "dph") -AnnotationAssertion( "2015-05-06T11:22:38Z") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0061695") -AnnotationAssertion(rdfs:label "transferase complex, transferring phosphorus-containing groups") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (secretory granule maturation) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "GOC:dph") Annotation( "PMID:16618809") "Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodeling.") @@ -47600,19 +46744,6 @@ AnnotationAssertion( "biological regulation") SubClassOf( ) -# Class: (regulation of molecular function) - -AnnotationAssertion(Annotation( "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( "biological_process") -AnnotationAssertion( "GO:0065009") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulation of molecular function") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (extracellular membrane-bounded organelle) AnnotationAssertion(Annotation( "GOC:isa_complete") "Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell.") @@ -48249,6 +47380,7 @@ AnnotationAssertion( "2010-03-08T03:56:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071705") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nitrogen compound transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -48349,6 +47481,7 @@ EquivalentClasses( ObjectIntersection # 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.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-10T01:39:16Z") AnnotationAssertion( "GO:0071841") @@ -48357,8 +47490,10 @@ AnnotationAssertion(Annotation( "cellular component organization or biogenesis at cellular level") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071840") +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 "cellular component organization or biogenesis") SubClassOf( ) @@ -48788,24 +47923,12 @@ AnnotationAssertion( "2009-05-06T04:51:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0080134") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of response to stress") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (intracellular amino acid homeostasis) - -AnnotationAssertion(Annotation( "PMID:19955263") "A homeostatic process involved in the maintenance of a steady state level of amino acids within a cell.") -AnnotationAssertion( "dhl") -AnnotationAssertion( "2010-01-27T04:47:27Z") -AnnotationAssertion( "amino acid homeostasis") -AnnotationAssertion( "cellular amino acid homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0080144") -AnnotationAssertion(rdfs:label "intracellular amino acid homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of fertilization) AnnotationAssertion(Annotation( "GOC:DHL") Annotation( "PMID:20478994") "Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).") @@ -48996,7 +48119,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0089718") AnnotationAssertion(rdfs:label "amino acid import across plasma membrane") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (positive regulation of microtubule nucleation) @@ -49296,10 +48419,13 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any cellular metabolic process involving nucleic acids.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26133"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27052"^^xsd:anyURI) AnnotationAssertion( "tb") AnnotationAssertion( "2010-04-07T10:18:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090304") +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 "nucleic acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -49382,26 +48508,6 @@ AnnotationAssertion(rdfs:label "RNA EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (positive regulation of brood size) - -AnnotationAssertion(Annotation( "GOC:rz") "Any process that increases brood size. Brood size is the number of progeny that survive embryogenesis and are cared for at one time.") -AnnotationAssertion( "tb") -AnnotationAssertion( "2016-12-19T15:07:32Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0090727") -AnnotationAssertion(rdfs:label "positive regulation of brood size") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of brood size) - -AnnotationAssertion(Annotation( "GOC:rz") "Any process that decreases brood size. Brood size is the number of progeny that survive embryogenesis and are cared for at one time.") -AnnotationAssertion( "tb") -AnnotationAssertion( "2016-12-19T15:07:32Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0090728") -AnnotationAssertion(rdfs:label "negative regulation of brood size") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (pigment granule membrane) AnnotationAssertion(Annotation( "PMID:11294610") "Any membrane that is part of a pigment granule.") @@ -49534,7 +48640,7 @@ AnnotationAssertion( "GO:0097164") AnnotationAssertion(rdfs:label "ammonium ion metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) # Class: (apoptotic signaling pathway) @@ -49577,30 +48683,6 @@ AnnotationAssertion(rdfs:label "olig EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (ammonium homeostasis) - -AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:12695560") "Any biological process involved in the maintenance of an internal steady state of ammonium.") -AnnotationAssertion( "pr") -AnnotationAssertion( "2012-03-22T02:51:22Z") -AnnotationAssertion( "ammonia homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0097272") -AnnotationAssertion(rdfs:label "ammonium homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (intracellular ammonium homeostasis) - -AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:12695560") "A homeostatic process involved in the maintenance of a steady state level of ammonium within a cell.") -AnnotationAssertion( "pr") -AnnotationAssertion( "2012-03-22T02:54:38Z") -AnnotationAssertion( "cellular ammonia homeostasis") -AnnotationAssertion( "cellular ammonium homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0097275") -AnnotationAssertion(rdfs:label "intracellular ammonium homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (protein localization to heterochromatin) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin.") @@ -49887,7 +48969,7 @@ AnnotationAssertion( AnnotationAssertion( "region of plasma membrane") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098590") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.") AnnotationAssertion(rdfs:label "plasma membrane region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -49944,17 +49026,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (monoatomic cation transmembrane transport) - -AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:vw") "The process in which a monoatomic cation is transported across a membrane. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom.") -AnnotationAssertion( "GO:0099132") -AnnotationAssertion( "cation transmembrane transport") -AnnotationAssertion( "ATP hydrolysis coupled cation transmembrane transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0098655") -AnnotationAssertion(rdfs:label "monoatomic cation transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) - # Class: (import into cell) AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.") @@ -50077,16 +49148,6 @@ AnnotationAssertion(rdfs:label "bone EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (inorganic ion homeostasis) - -AnnotationAssertion(Annotation( "GOC:dos") "Any process involved in the maintenance of an internal steady state of inorganic ions within an organism or cell.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0098771") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "inorganic ion homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (skin epidermis development) AnnotationAssertion(Annotation( "GOC:dos") "The process whose specific outcome is the progression of the skin epidermis over time, from its formation to the mature structure.") @@ -50506,7 +49567,7 @@ AnnotationAssertion( "GO:0099082") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retrograde trans-synaptic signaling by neuropeptide") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (retrograde trans-synaptic signaling by neuropeptide, modulating synaptic transmission) @@ -50516,7 +49577,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua.") AnnotationAssertion(rdfs:label "retrograde trans-synaptic signaling by neuropeptide, modulating synaptic transmission") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (microtubule polymerization based movement) @@ -50853,7 +49914,7 @@ AnnotationAssertion( "GO:0099538") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "synaptic signaling via neuropeptide") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (trans-synaptic signaling by neuropeptide) @@ -50862,7 +49923,7 @@ AnnotationAssertion( "GO:0099540") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trans-synaptic signaling by neuropeptide") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (trans-synaptic signaling by lipid) @@ -50903,7 +49964,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua.") AnnotationAssertion(rdfs:label "trans-synaptic signaling by neuropeptide, modulating synaptic transmission") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (trans-synaptic signaling by lipid, modulating synaptic transmission) @@ -51238,6 +50299,7 @@ AnnotationAssertion(Annotation( "kmv") AnnotationAssertion( "2018-01-29T14:46:52Z") AnnotationAssertion( "biological_process") +AnnotationAssertion( "endosomal trafficking") AnnotationAssertion( "GO:0110077") AnnotationAssertion(rdfs:label "vesicle-mediated intercellular transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -51675,57 +50737,6 @@ AnnotationAssertion(rdfs:label "orga SubClassOf( ) SubClassOf( ) -# Class: (catalytic activity, acting on a protein) - -AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify a protein.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2017-09-14T10:32:59Z") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0140096") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "catalytic activity, acting on a protein") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (catalytic activity, acting on DNA) - -AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify DNA.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2017-09-14T12:03:51Z") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0140097") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "catalytic activity, acting on DNA") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (catalytic activity, acting on RNA) - -AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21612"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2017-09-14T12:05:21Z") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0140098") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "catalytic activity, acting on RNA") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (catalytic activity, acting on a glycoprotein) - -AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalysis of a biochemical reaction at physiological temperatures in which one of the substrates is a glycoprotein.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2017-09-15T19:27:54Z") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0140103") -AnnotationAssertion(rdfs:label "catalytic activity, acting on a glycoprotein") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # 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.") @@ -51926,18 +50937,6 @@ AnnotationAssertion(rdfs:label "vacu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (catalytic activity, acting on a nucleic acid) - -AnnotationAssertion(Annotation( "GOC:pg") "Catalytic activity that acts to modify a nucleic acid.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21402"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2021-05-11T06:31:07Z") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0140640") -AnnotationAssertion(rdfs:label "catalytic activity, acting on a nucleic acid") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - # Class: (radial glia-guided pyramidal neuron migration) AnnotationAssertion(Annotation( "PMID:3760547") "The radial migration of a pyramidal neuron along radial glial cells.") @@ -51976,31 +50975,31 @@ AnnotationAssertion( "cytosol to Golgi apparatus transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -# Class: (multicellular organismal-level chemical homeostasis) - -AnnotationAssertion(Annotation( "GOC:curators") "A homeostatic process involved in the maintenance of a steady state level of a chemical within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24554"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2022-12-12T09:11:06Z") -AnnotationAssertion( "multicellular organism level chemical homeostasis") -AnnotationAssertion( "organismal level chemical homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0140962") -AnnotationAssertion(rdfs:label "multicellular organismal-level chemical homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (intracellular nitrogen homeostasis) - -AnnotationAssertion(Annotation( "GOC:tb") "A homeostatic process involved in the maintenance of a steady state level of nitrogen within a cell.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25558"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2023-06-15T08:56:16Z") -AnnotationAssertion( "cellular nitrogen homeostasis") -AnnotationAssertion( "nitrogen homeostasis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0141067") -AnnotationAssertion(rdfs:label "intracellular nitrogen homeostasis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (nucleic acid biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The biosynthetic process resulting in the formation of a nucleic acid.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27408"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2024-03-25T07:33:40Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0141187") +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 "nucleic acid biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (nucleic acid catabolic process) + +AnnotationAssertion(Annotation( "GOC:curators") "The cellular DNA metabolic process resulting in the breakdown of a nucleic acid.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27408"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2024-03-25T07:35:06Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0141188") +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 "nucleic acid catabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (regulation of postsynapse assembly) @@ -53464,12 +52463,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organonitrogen compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -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( "pr") AnnotationAssertion( "2012-11-04T15:18:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound anabolism") @@ -53478,6 +52477,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901566") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organonitrogen compound biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -53486,6 +52486,7 @@ SubClassOf( (organic substance biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-05T11:04:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity anabolism") @@ -53499,6 +52500,7 @@ AnnotationAssertion( "organic substance synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901576") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic substance biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -53644,7 +52646,7 @@ AnnotationAssertion( AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901652") AnnotationAssertion(rdfs:label "response to peptide") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (response to ketone) @@ -53703,22 +52705,28 @@ SubClassOf( (response to nitrogen compound) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "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 nitrogen compound stimulus.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:06:08Z") AnnotationAssertion( "response to nitrogen molecular entity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901698") +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 nitrogen compound") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (response to oxygen-containing compound) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "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 oxygen-containing compound stimulus.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:11:37Z") AnnotationAssertion( "response to oxygen molecular entity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901700") +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 oxygen-containing compound") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -54009,6 +53017,7 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cilium assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:dph") Annotation( "PMID:17719545") "Any process that modulates the frequency, rate or extent of cilium assembly.") +AnnotationAssertion( ) AnnotationAssertion( "dph") AnnotationAssertion( "2013-03-26T18:10:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ciliogenesis") @@ -54017,6 +53026,9 @@ AnnotationAssertion(Annotation( "GO:1902017") AnnotationAssertion(rdfs:label "regulation of cilium assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (negative regulation of cilium assembly) @@ -54676,19 +53688,6 @@ AnnotationAssertion( "positive regulation of protein localization to synapse") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (catalytic complex) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "PMID:8077207") "A protein complex which is capable of catalytic activity.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19980"^^xsd:anyURI) -AnnotationAssertion( "bhm") -AnnotationAssertion( "2013-11-13T16:18:47Z") -AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "GOC:jl") "enzyme complex") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:1902494") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "catalytic complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of organelle transport along microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "PMID:21147087") "Any process that modulates the frequency, rate or extent of organelle transport along microtubule.") @@ -57083,45 +56082,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (regulation of monoatomic cation transmembrane transport) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15304482") "Any process that modulates the frequency, rate or extent of cation transmembrane transport.") -AnnotationAssertion( "sl") -AnnotationAssertion( "2015-03-18T21:11:43Z") -AnnotationAssertion( "regulation of cation transmembrane transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1904062") -AnnotationAssertion(rdfs:label "regulation of monoatomic cation transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of cation transmembrane transport) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15304482") "Any process that stops, prevents or reduces the frequency, rate or extent of cation transmembrane transport.") -AnnotationAssertion( "sl") -AnnotationAssertion( "2015-03-18T21:11:50Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cation transmembrane transport") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cation transmembrane transport") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cation transmembrane transport") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cation transmembrane transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1904063") -AnnotationAssertion(rdfs:label "negative regulation of cation transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of cation transmembrane transport) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15304482") "Any process that activates or increases the frequency, rate or extent of cation transmembrane transport.") -AnnotationAssertion( "sl") -AnnotationAssertion( "2015-03-18T21:11:55Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cation transmembrane transport") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cation transmembrane transport") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cation transmembrane transport") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cation transmembrane transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1904064") -AnnotationAssertion(rdfs:label "positive regulation of cation transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of trophectodermal cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24508636") "Any process that modulates the frequency, rate or extent of trophectodermal cell proliferation.") @@ -58879,18 +57839,6 @@ AnnotationAssertion( "positive regulation of endothelial cell activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (transmembrane phosphate ion transport from cytosol to vacuole) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000078") Annotation( "PMID:26554016") "The directed movement of phosphate ions from the cytosol across the vacuolar membrane and into the vacuolar lumen.") -AnnotationAssertion( "tb") -AnnotationAssertion( "2016-03-03T00:34:12Z") -AnnotationAssertion( "GO:0007037") -AnnotationAssertion( "vacuolar phosphate transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905011") -AnnotationAssertion(rdfs:label "transmembrane phosphate ion transport from cytosol to vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) - # Class: (carboxylic acid transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000069") Annotation( "PMID:10869563") "The process in which carboxylic acid is transported across a membrane.") @@ -61293,16 +60241,6 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (transferase complex) - -AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:16540464") "A protein complex capable of catalyzing 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).") -AnnotationAssertion( "bhm") -AnnotationAssertion( "2013-11-12T13:20:12Z") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:1990234") -AnnotationAssertion(rdfs:label "transferase complex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (RNA localization to chromatin) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:mah") Annotation( "PMID:22582262") "A process in which RNA is transported to and maintained in a part of a chromosome that is organized into chromatin.") @@ -61671,39 +60609,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (regulation of phosphate transmembrane transport) - -AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of phosphate transmembrane transport.") -AnnotationAssertion( "vw") -AnnotationAssertion( "2010-10-15T11:33:04Z") -AnnotationAssertion( "regulation of phosphate membrane transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:2000185") -AnnotationAssertion(rdfs:label "regulation of phosphate transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (negative regulation of phosphate transmembrane transport) - -AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents, or reduces the frequency, rate or extent of phosphate transmembrane transport.") -AnnotationAssertion( "vw") -AnnotationAssertion( "2010-10-15T11:33:08Z") -AnnotationAssertion( "negative regulation of phosphate membrane transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:2000186") -AnnotationAssertion(rdfs:label "negative regulation of phosphate transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (positive regulation of phosphate transmembrane transport) - -AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of phosphate transmembrane transport.") -AnnotationAssertion( "vw") -AnnotationAssertion( "2010-10-15T11:33:10Z") -AnnotationAssertion( "positive regulation of phosphate membrane transport") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:2000187") -AnnotationAssertion(rdfs:label "positive regulation of phosphate transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of female gonad development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of female gonad development.") @@ -62834,6 +61739,7 @@ SubClassOf(Annotation( (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( ) AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-24T01:20:58Z") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of apoptotic signalling pathway") @@ -62841,7 +61747,10 @@ AnnotationAssertion( "GO:2001235") AnnotationAssertion(rdfs:label "positive regulation of apoptotic signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) # Class: (negative regulation of chromosome organization) @@ -63761,6 +62670,7 @@ SubClassOf( (Saccharomyces cerevisiae) AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:2898199") AnnotationAssertion( "NCBITaxon:41870") AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Saccharomyces cerevisiae 'var. diastaticus'") @@ -64126,7 +63036,7 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "protein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -64575,20 +63485,20 @@ EquivalentClasses( ObjectIntersecti SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (protein-containing material entity) - -AnnotationAssertion(Annotation( "PRO:DAN") "A material entity that minimally consists of a protein.") -AnnotationAssertion(Annotation( "PRO:DAN") "protein") -AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") -AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") -AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") -AnnotationAssertion( "protein") -AnnotationAssertion( "PR:000050567") -AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).") -AnnotationAssertion(rdfs:label "protein-containing material entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing molecular entity) + +AnnotationAssertion(Annotation( "PRO:DAN") "A molecular entity that minimally consists of a protein.") +AnnotationAssertion(Annotation( "PRO:DAN") "protein") +AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") +AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") +AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000064867") +AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565).") +AnnotationAssertion(rdfs:label "protein-containing molecular entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (T-cell surface glycoprotein CD8 alpha chain (mouse)) @@ -65213,7 +64123,6 @@ AnnotationAssertion( "zone of skin") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -65564,7 +64473,6 @@ AnnotationAssertion( "serous membrane") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -65716,7 +64624,6 @@ AnnotationAssertion(Annotation( "UBERON:0000058") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duct") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -66237,7 +65144,6 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000094") AnnotationAssertion(rdfs:label "membrane organ") -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA-def") ObjectSomeValuesFrom( )) @@ -66564,7 +65470,6 @@ AnnotationAssertion( "UBERON:0000117") AnnotationAssertion(rdfs:label "respiratory tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -66921,7 +65826,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "CL:tm") ObjectSomeValuesFrom( )) @@ -66994,7 +65898,6 @@ AnnotationAssertion(Annotation( "UBERON:0000304") AnnotationAssertion(rdfs:label "tendon sheath") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -67106,7 +66009,6 @@ AnnotationAssertion( "mucosa") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -68075,7 +66977,6 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -69045,7 +67946,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cornea") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) @@ -69454,10 +68354,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reproductive system") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg"^^xsd:anyURI) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -69486,7 +68386,6 @@ AnnotationAssertion( "BSA:0000079") AnnotationAssertion( "BTO:0000534") AnnotationAssertion( "EMAPA:17383") -AnnotationAssertion(Annotation( ) "FBbt:00004858") AnnotationAssertion( "FMA:18250") AnnotationAssertion( "GAID:368") AnnotationAssertion( "HAO:0000379") @@ -74426,7 +73325,6 @@ AnnotationAssertion( "capsule of lens") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -75321,7 +74219,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood plasma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -75589,7 +74486,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood vessel") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -76326,7 +75222,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dermis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -76374,7 +75269,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hypodermis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) @@ -76908,7 +75802,6 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_M_Skin.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -77492,7 +76385,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "integument") -SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -78310,7 +77202,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "exocrine system") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -78921,7 +77812,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "exocrine gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -79425,7 +78315,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pericardium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -79572,7 +78461,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "integumental system") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -80063,7 +78951,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tunica intima") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg"^^xsd:anyURI) -SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "check for exceptions, e.g. capillaries") ObjectSomeValuesFrom( )) @@ -81852,10 +80739,10 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reproductive organ") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female reproductive organ) @@ -87073,7 +85960,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiovascular system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -87097,7 +85983,6 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -87178,7 +86063,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arterial system") -SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -87233,7 +86117,6 @@ AnnotationAssertion( "UBERON:0004582") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "venous system") -SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -87545,7 +86428,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "paired limb/fin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "VSAO") ) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -90547,7 +89429,6 @@ AnnotationAssertion(Annotation( "UBERON:0005734") AnnotationAssertion(rdfs:label "tunica adventitia of blood vessel") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg"^^xsd:anyURI) -SubClassOf( ) SubClassOf(Annotation( "cjm") ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -90642,7 +89523,6 @@ AnnotationAssertion( "FMA:63872") "basement membrane") AnnotationAssertion( "UBERON:0005769") AnnotationAssertion(rdfs:label "basement membrane of epithelium") -SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -90892,7 +89772,6 @@ AnnotationAssertion( "UBERON:0005906") AnnotationAssertion(rdfs:comment "See notes for serous membrane") AnnotationAssertion(rdfs:label "serous sac") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -92389,7 +91268,6 @@ AnnotationAssertion( "UBERON:0006965") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vascular cord") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -92769,7 +91647,6 @@ AnnotationAssertion( "UBERON:0007195") AnnotationAssertion(rdfs:label "stroma of bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -93897,7 +92774,6 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0007845") AnnotationAssertion(rdfs:label "regular connective tissue") -SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -94246,7 +93122,6 @@ AnnotationAssertion( "UBERON:0008886") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary vascular system") -SubClassOf( ) SubClassOf(Annotation( "Obol") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -96640,7 +95515,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "meningeal cluster") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -96912,7 +95786,6 @@ AnnotationAssertion( "UBERON:0011234") AnnotationAssertion(rdfs:label "fibrous membrane of synovial tendon sheath") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -97349,7 +96222,6 @@ AnnotationAssertion( "UBERON:0011823") AnnotationAssertion(rdfs:label "dense connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -97399,7 +96271,6 @@ AnnotationAssertion( "UBERON:0011860") AnnotationAssertion(rdfs:label "collection of collagen fibrils") AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) SubClassOf(Annotation( "ZFA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -97587,7 +96458,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stomach glandular region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -97886,7 +96756,6 @@ AnnotationAssertion(Annotation( "Wikipedia:Fibrous_tunic_of_eyeball") "fibrous tunic") AnnotationAssertion( "UBERON:0012430") AnnotationAssertion(rdfs:label "tunica fibrosa of eyeball") -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ) @@ -100234,7 +99103,6 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0034929") AnnotationAssertion(rdfs:label "external soft tissue zone") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -101388,6 +100256,8 @@ SubClassOf( ObjectSomeValuesFrom( SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ) SubClassOf(Annotation( ) ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -101443,7 +100313,6 @@ SubClassOf(ObjectIntersectionOf( SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) @@ -101491,12 +100360,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -101518,35 +100382,9 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -101555,38 +100393,8 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file From ee24c8c1501299d27b9e4c840b65a3ed849dd3d2 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 10 Aug 2024 09:41:36 +0300 Subject: [PATCH 2/4] Undo import refresh, will be done in another context --- src/ontology/imports/merged_import.owl | 4002 +++++++++++++++--------- 1 file changed, 2597 insertions(+), 1405 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 29edf71..60eb6f0 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,19 +7,21 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-05-18") + +Annotation(owl:versionInfo "2024-03-28") 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()) @@ -51,6 +53,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -64,6 +67,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -95,6 +99,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -108,6 +116,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -138,6 +147,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -146,7 +157,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -179,12 +194,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -220,6 +233,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -233,6 +247,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -262,7 +278,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -309,8 +327,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -331,11 +349,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -369,12 +382,14 @@ 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()) @@ -786,6 +801,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -811,7 +827,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1050,6 +1065,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1115,9 +1132,15 @@ 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()) @@ -1126,6 +1149,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1331,6 +1356,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1405,6 +1432,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1511,6 +1539,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1519,21 +1549,26 @@ 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()) @@ -1671,6 +1706,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1716,6 +1752,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1774,6 +1812,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1787,6 +1826,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1817,6 +1857,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1829,6 +1870,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1892,8 +1934,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1920,6 +1965,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1950,6 +1996,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2020,6 +2067,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2061,6 +2111,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2106,6 +2158,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2125,10 +2178,13 @@ 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()) @@ -2224,6 +2280,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2242,6 +2300,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2256,6 +2316,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2451,6 +2512,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2482,9 +2544,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2550,6 +2614,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2579,6 +2647,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2675,8 +2746,13 @@ 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()) @@ -2730,6 +2806,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2934,6 +3011,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2957,6 +3035,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3055,6 +3134,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3104,6 +3184,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3117,6 +3199,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3146,6 +3230,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3158,6 +3243,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3307,6 +3393,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3323,11 +3413,12 @@ 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()) @@ -3495,6 +3586,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3624,6 +3716,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3711,6 +3806,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3844,6 +3940,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3875,6 +3972,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4122,7 +4222,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4251,7 +4350,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5933,10 +6032,14 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -5944,7 +6047,16 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6000,6 +6112,8 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6015,8 +6129,12 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6045,13 +6163,30 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6069,14 +6204,20 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6088,17 +6229,25 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6107,6 +6256,9 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -6162,6 +6314,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6207,21 +6360,19 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6275,6 +6426,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6323,7 +6475,9 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) +Declaration(AnnotationProperty(rdfs:seeAlso)) Declaration(AnnotationProperty(owl:deprecated)) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6338,7 +6492,7 @@ Declaration(AnnotationProperty()) AnnotationAssertion(rdfs:label "definition") -# Annotation Property: (has ontology root term) +# Annotation Property: (preferred_root) AnnotationAssertion( "IAO:0000700") AnnotationAssertion( "external") @@ -6347,6 +6501,7 @@ AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "has_ontology_root_term") AnnotationAssertion(rdfs:label "has ontology root term") +AnnotationAssertion(rdfs:label "preferred_root") # Annotation Property: (term replaced by) @@ -6457,6 +6612,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -6473,10 +6632,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -6501,10 +6656,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -6513,10 +6664,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -6721,6 +6868,12 @@ AnnotationAssertion(rdfs:label "shorthand") +# Annotation Property: rdfs:seeAlso (see also) + +AnnotationAssertion( rdfs:seeAlso "http://www.w3.org/2000/01/rdf-schema#seeAlso") +AnnotationAssertion( rdfs:seeAlso "seeAlso") +AnnotationAssertion(rdfs:label rdfs:seeAlso "see also") + ############################ # Object Properties @@ -6958,6 +7111,19 @@ AnnotationAssertion(rdfs:label "has ObjectPropertyDomain( ) ObjectPropertyRange( ) +# Object Property: (function of) + +AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) +AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "function_of"@en) +AnnotationAssertion( "is function of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "function of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + # Object Property: (quality of) AnnotationAssertion( "this red color is a quality of this apple"@en) @@ -6982,6 +7148,17 @@ AnnotationAssertion(rdfs:label "role SubObjectPropertyOf( ) InverseObjectProperties( ) +# Object Property: (has function) + +AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "has_function"@en) +AnnotationAssertion(rdfs:label "has function"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (has quality) AnnotationAssertion( "this apple has quality this red color"@en) @@ -7003,6 +7180,23 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) +# Object Property: (has disposition) + +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) +AnnotationAssertion(rdfs:label "has disposition"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (disposition of) + +AnnotationAssertion( "inverse of has disposition") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "disposition of"@en) +SubObjectPropertyOf( ) + # Object Property: (location of) AnnotationAssertion( "is location of"@en) @@ -7108,6 +7302,61 @@ SubObjectPropertyOf( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ) +# Object Property: (has regulatory component activity) + +AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) +AnnotationAssertion( "RO:0002013") +AnnotationAssertion( "external") +AnnotationAssertion( "has_regulatory_component_activity") +AnnotationAssertion( "has_regulatory_component_activity") +AnnotationAssertion(rdfs:label "has regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has negative regulatory component activity) + +AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) +AnnotationAssertion( "RO:0002014") +AnnotationAssertion( "external") +AnnotationAssertion( "has_negative_regulatory_component_activity") +AnnotationAssertion( "has_negative_regulatory_component_activity") +AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") +AnnotationAssertion(rdfs:label "has negative regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has positive regulatory component activity) + +AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") +AnnotationAssertion(rdfs:label "has positive regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has component activity) + +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") +AnnotationAssertion(rdfs:label "has component activity") +SubObjectPropertyOf( ) + +# Object Property: (has component process) + +AnnotationAssertion( "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "has component process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (occurs across) AnnotationAssertion( "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.") @@ -7116,6 +7365,43 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "occurs across") SubObjectPropertyOf( ) +# Object Property: (directly regulated by) + +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(rdfs:label "directly regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly negatively regulated by) + +AnnotationAssertion(Annotation( ) "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly negatively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly positively regulated by) + +AnnotationAssertion(Annotation( ) "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly positively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has effector activity) + +AnnotationAssertion(Annotation( ) "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") +AnnotationAssertion(rdfs:label "has effector activity") +SubObjectPropertyOf( ) +FunctionalObjectProperty() + # Object Property: (before or simultaneous with) AnnotationAssertion( "David Osumi-Sutherland") @@ -7912,6 +8198,25 @@ InverseObjectProperties( ) ObjectPropertyRange( ) +# Object Property: (acts upstream of) + +AnnotationAssertion( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") +AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within) + +AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") +AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") +AnnotationAssertion( "affects") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) +SubObjectPropertyOf( ) + # Object Property: (developmentally replaces) AnnotationAssertion( ) @@ -8120,6 +8425,23 @@ AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development") AnnotationAssertion(rdfs:label "developmentally related to"@en) +# Object Property: (enables) + +AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") +AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") +AnnotationAssertion( ) +AnnotationAssertion( "catalyzes") +AnnotationAssertion( "executes") +AnnotationAssertion( "has") +AnnotationAssertion( "is catalyzing") +AnnotationAssertion( "is executing") +AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enables"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + # Object Property: (functionally related to) AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") @@ -8135,6 +8457,44 @@ AnnotationAssertion( "part of structure that is capable of"@en) SubObjectPropertyOf( ) +# Object Property: (involved in) + +AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") +AnnotationAssertion( ) +AnnotationAssertion( "actively involved in") +AnnotationAssertion( "enables part of") +AnnotationAssertion(rdfs:label "involved in"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (regulates levels of) + +AnnotationAssertion( "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid") +AnnotationAssertion( "p regulates levels of c if p regulates some amount (PATO:0000070) of c") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "regulates levels of (process to entity)") +AnnotationAssertion( "RO:0002332") +AnnotationAssertion( "external") +AnnotationAssertion( "regulates_levels_of") +AnnotationAssertion( "regulates_levels_of") +AnnotationAssertion(rdfs:label "regulates levels of"@en) +AnnotationAssertion(rdfs:label "regulates levels of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (enabled by) + +AnnotationAssertion( "inverse of enables") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + # Object Property: (regulated by) AnnotationAssertion( "inverse of regulates") @@ -8287,6 +8647,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has member"@en) SubObjectPropertyOf( ) +IrreflexiveObjectProperty() # Object Property: (input of) @@ -8467,6 +8828,44 @@ SubObjectPropertyOf( ) InverseObjectProperties( ) +# Object Property: (immediately causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002405") +AnnotationAssertion( "external") +AnnotationAssertion( "immediately_causally_downstream_of") +AnnotationAssertion( "immediately_causally_downstream_of") +AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) +AnnotationAssertion(rdfs:label "immediately causally downstream of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (indirectly positively regulates) + +AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "indirectly activates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (indirectly negatively regulates) + +AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "indirectly inhibits") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + # Object Property: (causally related to) AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") @@ -8505,6 +8904,20 @@ SubObjectPropertyOf( ) TransitiveObjectProperty() +# Object Property: (immediately causally upstream of) + +AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002412") +AnnotationAssertion( "external") +AnnotationAssertion( "immediately_causally_upstream_of") +AnnotationAssertion( "immediately_causally_upstream_of") +AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) +AnnotationAssertion(rdfs:label "immediately causally upstream of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + # Object Property: (causally upstream of or within) AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") @@ -8535,6 +8948,54 @@ AnnotationAssertion(rdfs:label "caus SubObjectPropertyOf( ) TransitiveObjectProperty() +# Object Property: (involved in regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (involved in positive regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in positive regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in negative regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in negative regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in or involved in regulation of) + +AnnotationAssertion( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") +AnnotationAssertion( "OWL does not allow defining object properties via a Union") +AnnotationAssertion( ) +AnnotationAssertion( "involved in or reguates") +AnnotationAssertion(rdfs:label "involved in or involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (is active in) + +AnnotationAssertion( "A protein that enables activity in a cytosol.") +AnnotationAssertion(Annotation( ) Annotation( ) "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") +AnnotationAssertion( ) +AnnotationAssertion( "executes activity in") +AnnotationAssertion( "enables activity in") +AnnotationAssertion(rdfs:comment "") +AnnotationAssertion(rdfs:label "is active in") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Is_active_in"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + # Object Property: (contributes to morphology of) AnnotationAssertion( "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.") @@ -8542,6 +9003,88 @@ AnnotationAssertion( "contributes to morphology of") SubObjectPropertyOf( ) +# Object Property: (interacts with) + +AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") +AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) +AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion( ) +AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") +AnnotationAssertion( "in pairwise interaction with") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "interacts with") +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) +SymmetricObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (molecularly interacts with) + +AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") +AnnotationAssertion( ) +AnnotationAssertion( "binds") +AnnotationAssertion( "molecularly binds with") +AnnotationAssertion(rdfs:label "molecularly interacts with") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (phosphorylates) + +AnnotationAssertion( "Axiomatization to GO to be added later") +AnnotationAssertion( ) +AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") +AnnotationAssertion(rdfs:label "phosphorylates") +SubObjectPropertyOf( ) + +# Object Property: (directly regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "molecularly controls") +AnnotationAssertion(rdfs:label "directly regulates activity of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly negatively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly inhibits") +AnnotationAssertion( "molecularly decreases activity of") +AnnotationAssertion(rdfs:label "directly negatively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly positively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly activates") +AnnotationAssertion( "molecularly increases activity of") +AnnotationAssertion(rdfs:label "directly positively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (helper property (not for use in curation)) + +AnnotationAssertion( ) +AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") +AnnotationAssertion(rdfs:label "helper property (not for use in curation)") + # Object Property: (composed primarily of) AnnotationAssertion( "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'") @@ -8564,6 +9107,12 @@ AnnotationAssertion(rdfs:label "has ObjectPropertyDomain( ) ObjectPropertyRange( ) +# Object Property: (is kinase activity) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "is kinase activity") +SubObjectPropertyOf( ) + # Object Property: (receives input from) AnnotationAssertion( "See notes for inverse relation") @@ -8704,6 +9253,17 @@ AnnotationAssertion( "towards") SubObjectPropertyOf( ) +# Object Property: (causal relation between entities) + +AnnotationAssertion( "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between entities") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (has skeleton) AnnotationAssertion( "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'") @@ -8715,9 +9275,33 @@ AnnotationAssertion(rdfs:label "has SubObjectPropertyOf( ) InverseObjectProperties( ) AsymmetricObjectProperty() +IrreflexiveObjectProperty() ObjectPropertyDomain( ) ObjectPropertyRange(Annotation( "This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.") ) +# Object Property: (causally influenced by) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally influenced by (entity-centric)") +AnnotationAssertion(rdfs:label "causally influenced by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (interaction relation helper property) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "interaction relation helper property") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (molecular interaction relation helper property) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "molecular interaction relation helper property") +SubObjectPropertyOf( ) + # Object Property: (results in movement of) AnnotationAssertion( "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c") @@ -8733,6 +9317,18 @@ AnnotationAssertion( "results in movement of") SubObjectPropertyOf( ) +# Object Property: (causally influences) + +AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally influences (entity-centric)") +AnnotationAssertion(rdfs:label "causally influences") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (biomechanically related to) AnnotationAssertion( "A relation that holds between elements of a musculoskeletal system or its analogs.") @@ -8795,6 +9391,24 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) +# Object Property: (directly regulates) + +AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly regulates (processual)") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002578") +AnnotationAssertion( "external") +AnnotationAssertion( "directly_regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly_regulates") +AnnotationAssertion(rdfs:label "directly regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + # Object Property: (has part structure that is capable of) AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") @@ -8895,6 +9509,42 @@ AnnotationAssertion( "Groups both positive and negative correlation") AnnotationAssertion(rdfs:label "correlated with") +# Object Property: (directly positively regulates) + +AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002629") +AnnotationAssertion( "external") +AnnotationAssertion( "directly_positively_regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly_positively_regulates") +AnnotationAssertion(rdfs:label "directly positively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (directly negatively regulates) + +AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0002630") +AnnotationAssertion( "external") +AnnotationAssertion( "directly_negatively_regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly_negatively_regulates") +AnnotationAssertion(rdfs:label "directly negatively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + # Object Property: (produces) AnnotationAssertion( ) @@ -8968,15 +9618,57 @@ AnnotationAssertion(rdfs:label "has SubObjectPropertyOf( ) SubObjectPropertyOf( ) -# Object Property: (realized in response to stimulus) - -AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-12-26T19:45:49Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "realized in response to stimulus") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +# Object Property: (enables subfunction) + +AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "enables subfunction") +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, positive effect) + +AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, negative effect) + +AnnotationAssertion( "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) # Object Property: (causally upstream of or within, negative effect) @@ -8996,22 +9688,14 @@ AnnotationAssertion(rdfs:label "caus AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) -# Object Property: (realized in response to) - -AnnotationAssertion( "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.") -AnnotationAssertion( "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") -AnnotationAssertion( "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.") -AnnotationAssertion( "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "triggered by process") -AnnotationAssertion(rdfs:label "realized in response to"@en) -AnnotationAssertion(rdfs:seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +# Object Property: (regulates activity of) + +AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) # Object Property: (acts on population of) @@ -9044,6 +9728,23 @@ AnnotationAssertion(rdfs:label "resu AnnotationAssertion(rdfs:label "results in fusion of") SubObjectPropertyOf( ) +# Object Property: (indirectly causally upstream of) + +AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") +AnnotationAssertion( ) +AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) +SubObjectPropertyOf( ) + +# Object Property: (indirectly regulates) + +AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + # Object Property: (different in magnitude relative to) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") @@ -9094,14 +9795,49 @@ AnnotationAssertion(rdfs:label "reci AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) +# Object Property: (regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0019000") +AnnotationAssertion( "gene_ontology") +AnnotationAssertion( "regulates_characteristic") +AnnotationAssertion( "regulates_characteristic") +AnnotationAssertion(rdfs:label "regulates characteristic") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (positively regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0019001") +AnnotationAssertion( "gene_ontology") +AnnotationAssertion( "positively_regulates_characteristic") +AnnotationAssertion( "positively_regulates_characteristic") +AnnotationAssertion(rdfs:label "positively regulates characteristic") +SubObjectPropertyOf( ) + +# Object Property: (negatively regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion( "RO:0019002") +AnnotationAssertion( "gene_ontology") +AnnotationAssertion( "negatively_regulates_characteristic") +AnnotationAssertion( "negatively_regulates_characteristic") +AnnotationAssertion(rdfs:label "negatively regulates characteristic") +SubObjectPropertyOf( ) + # Object Property: (results in changes to anatomical or cellular structure) AnnotationAssertion( "p has anatomical participant c iff p has participant c, and c is an anatomical entity") @@ -9236,20 +9972,93 @@ AnnotationAssertion(rdfs:seeAlso () +# Class: (continuant) +AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: () +# Class: (occurrent) +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: () +# Class: (independent continuant) + +AnnotationAssertion( "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) + +# Class: (spatial region) + +AnnotationAssertion(rdfs:label "spatial region"@en) +SubClassOf( ) + +# Class: (process) + +AnnotationAssertion( "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) + +# Class: (quality) + +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (role) + +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (function) + +AnnotationAssertion(rdfs:label "function"@en) +SubClassOf( ) +# Class: (material entity) + +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) +DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: () +# Class: (immaterial entity) +AnnotationAssertion(rdfs:label "immaterial entity"@en) +SubClassOf( ) DisjointClasses( ObjectSomeValuesFrom( )) # Class: (electron) @@ -10189,6 +10998,43 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (phosphate(3-)) + +AnnotationAssertion( "A phosphate ion that is the conjugate base of hydrogenphosphate.") +AnnotationAssertion( "-3") +AnnotationAssertion( "O4P") +AnnotationAssertion( "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3") +AnnotationAssertion( "NBIIXXVUZAFLBC-UHFFFAOYSA-K") +AnnotationAssertion( "94.97136") +AnnotationAssertion( "94.95507") +AnnotationAssertion( "[O-]P([O-])([O-])=O") +AnnotationAssertion( "CHEBI:14791") +AnnotationAssertion( "CHEBI:45024") +AnnotationAssertion( "CHEBI:7793") +AnnotationAssertion(Annotation( "Beilstein") "Beilstein:3903772") +AnnotationAssertion(Annotation( "ChemIDplus") "CAS:14265-44-2") +AnnotationAssertion(Annotation( "KEGG COMPOUND") "CAS:14265-44-2") +AnnotationAssertion(Annotation( "Gmelin") "Gmelin:1997") +AnnotationAssertion( "KEGG:C00009") +AnnotationAssertion(Annotation( "ChEBI") "PDBeChem:PO4") +AnnotationAssertion(Annotation( "Reaxys") "Reaxys:3903772") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "phosphate") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "tetraoxidophosphate(3-)") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "tetraoxophosphate(3-)") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "tetraoxophosphate(V)") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Orthophosphate") +AnnotationAssertion(Annotation( "PDBeChem") "PHOSPHATE ION") +AnnotationAssertion(Annotation( "IUPAC") "PO4(3-)") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Phosphate") +AnnotationAssertion(Annotation( "IUPAC") "[PO4](3-)") +AnnotationAssertion( "CHEBI:18367") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphate(3-)") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (acyl group) AnnotationAssertion( "An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.") @@ -10381,6 +11227,16 @@ AnnotationAssertion( "drug") SubClassOf( ) +# Class: (monoatomic cation) + +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "monoatomic cations") +AnnotationAssertion( "CHEBI:23906") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "monoatomic cation") +SubClassOf( ) +SubClassOf( ) + # Class: (enzyme inhibitor) AnnotationAssertion( "A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.") @@ -10787,6 +11643,93 @@ AnnotationAssertion(rdfs:label "pep SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (phosphate) + +AnnotationAssertion( "Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "phosphates") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "phosphates") +AnnotationAssertion( "CHEBI:26020") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphate") +SubClassOf( ) + +# Class: (phosphoric acid) + +AnnotationAssertion( "A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom.") +AnnotationAssertion( "0") +AnnotationAssertion( "H3O4P") +AnnotationAssertion( "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)") +AnnotationAssertion( "NBIIXXVUZAFLBC-UHFFFAOYSA-N") +AnnotationAssertion( "97.99520") +AnnotationAssertion( "97.97690") +AnnotationAssertion( "[H]OP(=O)(O[H])O[H]") +AnnotationAssertion(Annotation( "Beilstein") "Beilstein:1921286") +AnnotationAssertion(Annotation( "ChemIDplus") "CAS:7664-38-2") +AnnotationAssertion(Annotation( "KEGG COMPOUND") "CAS:7664-38-2") +AnnotationAssertion(Annotation( "NIST Chemistry WebBook") "CAS:7664-38-2") +AnnotationAssertion(Annotation( "DrugCentral") "Drug_Central:4478") +AnnotationAssertion(Annotation( "Gmelin") "Gmelin:2000") +AnnotationAssertion( "HMDB:HMDB0002142") +AnnotationAssertion( "KEGG:C00009") +AnnotationAssertion( "KEGG:D05467") +AnnotationAssertion( "KNApSAcK:C00007408") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:11455380") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:15630224") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:17439666") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:17518491") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:22282755") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:22333268") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:22381614") +AnnotationAssertion(Annotation( "Europe PMC") "PMID:22401268") +AnnotationAssertion(Annotation( "Reaxys") "Reaxys:1921286") +AnnotationAssertion( "Wikipedia:Phosphoric_Acid") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Phosphoric acid") +AnnotationAssertion(Annotation( "IUPAC") "phosphoric acid") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "tetraoxophosphoric acid") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "trihydrogen tetraoxophosphate(3-)") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "trihydroxidooxidophosphorus") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "IUPAC") "H3PO4") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Orthophosphoric acid") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Phosphate") +AnnotationAssertion(Annotation( "ChEBI") "Phosphorsaeure") +AnnotationAssertion(Annotation( "ChEBI") "Phosphorsaeureloesungen") +AnnotationAssertion(Annotation( "IUPAC") "[PO(OH)3]") +AnnotationAssertion(Annotation( "ChEBI") "acide phosphorique") +AnnotationAssertion(Annotation( "ChEBI") "acidum phosphoricum") +AnnotationAssertion(Annotation( "NIST_Chemistry_WebBook") "orthophosphoric acid") +AnnotationAssertion( "CHEBI:26078") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphoric acid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphoric acid derivative) + +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion( "CHEBI:26079") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphoric acid derivative") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphorus molecular entity) + +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "phosphorus molecular entities") +AnnotationAssertion( "CHEBI:26082") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphorus molecular entity") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (steroid hormone) AnnotationAssertion( "Any steroid that acts as hormone.") @@ -11066,6 +12009,39 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (phosphorus atom) + +AnnotationAssertion( "0") +AnnotationAssertion( "P") +AnnotationAssertion( "InChI=1S/P") +AnnotationAssertion( "OAICVXFJPJFONN-UHFFFAOYSA-N") +AnnotationAssertion( "30.97376") +AnnotationAssertion( "30.97376") +AnnotationAssertion( "[P]") +AnnotationAssertion( "CHEBI:26080") +AnnotationAssertion( "CHEBI:8168") +AnnotationAssertion(Annotation( "ChemIDplus") "CAS:7723-14-0") +AnnotationAssertion(Annotation( "KEGG COMPOUND") "CAS:7723-14-0") +AnnotationAssertion(Annotation( "Gmelin") "Gmelin:16235") +AnnotationAssertion( "KEGG:C06262") +AnnotationAssertion( "WebElements:P") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "phosphorus") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "IUPAC") "15P") +AnnotationAssertion(Annotation( "IUPAC") "P") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "P") +AnnotationAssertion(Annotation( "ChEBI") "Phosphor") +AnnotationAssertion(Annotation( "KEGG_COMPOUND") "Phosphorus") +AnnotationAssertion(Annotation( "ChEBI") "fosforo") +AnnotationAssertion(Annotation( "ChEBI") "phosphore") +AnnotationAssertion(Annotation( "ChEBI") "phosphorus") +AnnotationAssertion( "CHEBI:28659") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphorus atom") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (serotonin) AnnotationAssertion( "A primary amino compound that is the 5-hydroxy derivative of tryptamine.") @@ -11441,8 +12417,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic group") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (organyl group) @@ -11624,6 +12599,31 @@ AnnotationAssertion( "heteroorganic entity") SubClassOf( ) +# Class: (agrochemical) + +AnnotationAssertion( "An agrochemical is a substance that is used in agriculture or horticulture.") +AnnotationAssertion( "Wikipedia:Agrochemical") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "agrichemical") +AnnotationAssertion(Annotation( "ChEBI") "agrichemicals") +AnnotationAssertion(Annotation( "ChEBI") "agricultural chemicals") +AnnotationAssertion(Annotation( "ChEBI") "agrochemicals") +AnnotationAssertion( "CHEBI:33286") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "agrochemical") +SubClassOf( ) + +# Class: (fertilizer) + +AnnotationAssertion( "A fertilizer is any substance that is added to soil or water to assist the growth of plants.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "fertiliser") +AnnotationAssertion(Annotation( "ChEBI") "fertilizers") +AnnotationAssertion( "CHEBI:33287") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "fertilizer") +SubClassOf( ) + # Class: (pnictogen) AnnotationAssertion( "Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.") @@ -11750,6 +12750,17 @@ AnnotationAssertion(rdfs:label "sul SubClassOf( ) SubClassOf( ) +# Class: (pnictogen oxoacid) + +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "pnictogen oxoacids") +AnnotationAssertion( "CHEBI:33408") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "pnictogen oxoacid") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (sulfur oxoacid derivative) AnnotationAssertion(Annotation( "ChEBI") "sulfur oxoacid derivative") @@ -11761,6 +12772,44 @@ AnnotationAssertion(rdfs:label "sul SubClassOf( ) SubClassOf( ) +# Class: (phosphorus oxoacid) + +AnnotationAssertion( "A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons.") +AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoacid") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "Oxosaeure des Phosphors") +AnnotationAssertion(Annotation( "ChEBI") "oxoacids of phosphorus") +AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoacids") +AnnotationAssertion( "CHEBI:33457") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphorus oxoacid") +SubClassOf( ) +SubClassOf( ) + +# Class: (pnictogen oxoanion) + +AnnotationAssertion(Annotation( "ChEBI") "pnictogen oxoanion") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "pnictogen oxoanions") +AnnotationAssertion( "CHEBI:33459") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "pnictogen oxoanion") +SubClassOf( ) +SubClassOf( ) + +# Class: (phosphorus oxoanion) + +AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoanion") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "oxoanions of phosphorus") +AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoanions") +AnnotationAssertion( "CHEBI:33461") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphorus oxoanion") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + # Class: (sulfur oxoanion) AnnotationAssertion(Annotation( "ChEBI") "sulfur oxoanion") @@ -11934,7 +12983,7 @@ SubClassOf( ObjectSomeValuesFrom( "A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.") AnnotationAssertion( "0") AnnotationAssertion( "CHO2R") -AnnotationAssertion( "45.017") +AnnotationAssertion( "45.01740") AnnotationAssertion( "44.99765") AnnotationAssertion( "OC([*])=O") AnnotationAssertion( "CHEBI:13428") @@ -12214,19 +13263,6 @@ AnnotationAssertion(rdfs:label "pol SubClassOf( ) SubClassOf( ) -# Class: (amino-acid cation) - -AnnotationAssertion(Annotation( "ChEBI") "amino-acid cation") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "amino acid cation") -AnnotationAssertion(Annotation( "ChEBI") "amino-acid cations") -AnnotationAssertion( "CHEBI:33703") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "amino-acid cation") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (alpha-amino acid) AnnotationAssertion( "An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.") @@ -12253,7 +13289,6 @@ AnnotationAssertion( "alpha-amino acid") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (amino-acid residue) @@ -12267,8 +13302,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino-acid residue") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (amino acid) @@ -12288,7 +13321,6 @@ AnnotationAssertion(rdfs:label "ami SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (alpha-amino-acid residue) @@ -12307,18 +13339,6 @@ AnnotationAssertion(rdfs:label "alp SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (alpha-amino-acid cation) - -AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid cation") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "alpha-amino acid cations") -AnnotationAssertion(Annotation( "ChEBI") "alpha-amino-acid cations") -AnnotationAssertion( "CHEBI:33719") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "alpha-amino-acid cation") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (carbohydrate acid) AnnotationAssertion(Annotation( "ChEBI") "carbohydrate acid") @@ -12813,6 +13833,20 @@ AnnotationAssertion(rdfs:label "mon SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (phosphate ion) + +AnnotationAssertion( "A phosphorus oxoanion that is the conjugate base of phosphoric acid.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "Pi") +AnnotationAssertion(Annotation( "ChEBI") "phosphate") +AnnotationAssertion(Annotation( "ChEBI") "phosphate ions") +AnnotationAssertion( "CHEBI:35780") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphate ion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (pnictogen hydride) AnnotationAssertion(Annotation( "ChEBI") "pnictogen hydride") @@ -12955,6 +13989,25 @@ AnnotationAssertion(rdfs:label "pol SubClassOf( ) SubClassOf( ) +# Class: (phosphorus oxoacid derivative) + +AnnotationAssertion(Annotation( "ChEBI") "phosphorus oxoacid derivative") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion( "CHEBI:36359") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphorus oxoacid derivative") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (phosphorus oxoacids and derivatives) + +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion( "CHEBI:36360") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphorus oxoacids and derivatives") +SubClassOf( ) + # Class: (carbonyl compound) AnnotationAssertion( "Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.") @@ -13347,6 +14400,38 @@ AnnotationAssertion(rdfs:label "Lew SubClassOf( ) SubClassOf( ) +# Class: (dihydrogenphosphate) + +AnnotationAssertion( "A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated.") +AnnotationAssertion( "-1") +AnnotationAssertion( "H2O4P") +AnnotationAssertion( "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-1") +AnnotationAssertion( "NBIIXXVUZAFLBC-UHFFFAOYSA-M") +AnnotationAssertion( "96.98724") +AnnotationAssertion( "96.96962") +AnnotationAssertion( "[H]OP([O-])(=O)O[H]") +AnnotationAssertion( "CHEBI:29137") +AnnotationAssertion( "CHEBI:39739") +AnnotationAssertion( "DrugBank:DB02831") +AnnotationAssertion(Annotation( "Gmelin") "Gmelin:1999") +AnnotationAssertion( "PDBeChem:2HP") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydrogen(tetraoxidophosphate)(1-)") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydrogenphosphate") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydrogentetraoxophosphate(1-)") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydrogentetraoxophosphate(V)") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "dihydroxidodioxidophosphate(1-)") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "PDBeChem") "DIHYDROGENPHOSPHATE ION") +AnnotationAssertion(Annotation( "IUPAC") "H2PO4(-)") +AnnotationAssertion(Annotation( "IUPAC") "[PO2(OH)2](-)") +AnnotationAssertion( "CHEBI:39745") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "dihydrogenphosphate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (hydroxy group) AnnotationAssertion( "0") @@ -13369,6 +14454,45 @@ AnnotationAssertion( "hydroxy group") SubClassOf( ) +# Class: (hydrogenphosphate) + +AnnotationAssertion( "A phosphate ion that is the conjugate base of dihydrogenphosphate.") +AnnotationAssertion( "-2") +AnnotationAssertion( "HO4P") +AnnotationAssertion( "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-2") +AnnotationAssertion( "NBIIXXVUZAFLBC-UHFFFAOYSA-L") +AnnotationAssertion( "95.97930") +AnnotationAssertion( "95.96234") +AnnotationAssertion( "OP([O-])([O-])=O") +AnnotationAssertion( "CHEBI:29139") +AnnotationAssertion( "CHEBI:43470") +AnnotationAssertion(Annotation( "Gmelin") "Gmelin:1998") +AnnotationAssertion( "MolBase:1628") +AnnotationAssertion( "PDBeChem:PI") +AnnotationAssertion( "PDBeChem:PO4") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydrogen(tetraoxidophosphate)(2-)") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydrogenphosphate") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydrogentetraoxophosphate(2-)") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydrogentetraoxophosphate(V)") +AnnotationAssertion(Annotation( "IUPAC") Annotation( ) "hydroxidotrioxidophosphate(2-)") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "IUPAC") "HPO4(2-)") +AnnotationAssertion(Annotation( "PDBeChem") "HYDROGENPHOSPHATE ION") +AnnotationAssertion(Annotation( "PDBeChem") "INORGANIC PHOSPHATE GROUP") +AnnotationAssertion(Annotation( "MolBase") "[P(OH)O3](2-)") +AnnotationAssertion(Annotation( "IUPAC") "[PO3(OH)](2-)") +AnnotationAssertion(Annotation( "ChEBI") "hydrogen phosphate") +AnnotationAssertion(Annotation( "UniProt") "phosphate") +AnnotationAssertion( "CHEBI:43474") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "hydrogenphosphate") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (hydrogensulfate) AnnotationAssertion( "-1") @@ -13700,6 +14824,7 @@ AnnotationAssertion( "CHEBI:50906") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "role") +SubClassOf( ) # Class: (neurotoxin) @@ -13996,23 +15121,6 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (cationic amino-acid residue) - -AnnotationAssertion( "An amino-acid residue protonated on nitrogen.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "amino acid cation residue") -AnnotationAssertion(Annotation( "ChEBI") "amino acid cation residues") -AnnotationAssertion(Annotation( "ChEBI") "amino-acid cation residue") -AnnotationAssertion(Annotation( "ChEBI") "amino-acid cation residues") -AnnotationAssertion(Annotation( "ChEBI") "cationic amino acid residue") -AnnotationAssertion(Annotation( "ChEBI") "cationic amino acid residues") -AnnotationAssertion(Annotation( "ChEBI") "cationic amino-acid residues") -AnnotationAssertion( "CHEBI:58942") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cationic amino-acid residue") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (organosulfate oxoanion) AnnotationAssertion( "An organic anion of general formula RS(=O)2O(-) where R is an organyl group.") @@ -14031,6 +15139,15 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (phosphoric acids) + +AnnotationAssertion( "Compounds containing one or more phosphoric acid units.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion( "CHEBI:59698") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphoric acids") +SubClassOf( ) + # Class: (nucleophilic reagent) AnnotationAssertion( "A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.") @@ -14317,65 +15434,6 @@ AnnotationAssertion( "organic acid") SubClassOf( ) -# Class: (cationic group) - -AnnotationAssertion( "A group that carries an overall positive charge.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "cationic groups") -AnnotationAssertion( "CHEBI:64766") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cationic group") -SubClassOf( ) - -# Class: (anionic group) - -AnnotationAssertion( "A group that carries an overall negative charge.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "anionic groups") -AnnotationAssertion( "CHEBI:64767") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anionic group") -SubClassOf( ) - -# Class: (organic cationic group) - -AnnotationAssertion( "A cationic group that contains carbon.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "organic cationic groups") -AnnotationAssertion( "CHEBI:64769") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organic cationic group") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (organic anionic group) - -AnnotationAssertion( "An anionic group that contains carbon.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "organic anionic groups") -AnnotationAssertion( "CHEBI:64775") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organic anionic group") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (anionic amino-acid residue) - -AnnotationAssertion( "An amino-acid residue carrying an overall negative charge.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI") "amino acid anion residue") -AnnotationAssertion(Annotation( "ChEBI") "amino acid anion residues") -AnnotationAssertion(Annotation( "ChEBI") "amino-acid anion residue") -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") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (poison) AnnotationAssertion( "Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.") @@ -14854,6 +15912,16 @@ AnnotationAssertion( "carbohydrates and carbohydrate derivatives") SubClassOf( ) +# Class: (trivalent inorganic anion) + +AnnotationAssertion( "Any inorganic anion with a valency of three.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "trivalent inorganic anions") +AnnotationAssertion( "CHEBI:79387") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "trivalent inorganic anion") +SubClassOf( ) + # Class: (divalent inorganic anion) AnnotationAssertion( "Any inorganic anion with a valency of two.") @@ -14915,11 +15983,21 @@ AnnotationAssertion(rdfs:label "hyd SubClassOf( ) SubClassOf( ) +# Class: (algal metabolite) + +AnnotationAssertion( "Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "algal metabolites") +AnnotationAssertion( "CHEBI:84735") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "algal metabolite") +SubClassOf( ) + # Class: (cell) AnnotationAssertion(Annotation( "CARO:mah") "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") AnnotationAssertion( "CALOHA:TS-2035") -AnnotationAssertion(Annotation( ) "FBbt:00007002") +AnnotationAssertion( "FBbt:00007002") AnnotationAssertion( "FMA:68646") AnnotationAssertion( "GO:0005623") AnnotationAssertion( "KUPO:0000002") @@ -14927,7 +16005,6 @@ AnnotationAssertion( "VHOG:0001533") AnnotationAssertion( "WBbt:0004017") AnnotationAssertion( "XAO:0003012") -AnnotationAssertion(Annotation( ) "ZFA:0009000") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).") @@ -14938,57 +16015,48 @@ DisjointClasses( ) DisjointClasses( ) -# Class: (neural crest derived fibroblast) +# Class: (fibroblast neural crest derived) -AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-5208-3432") "Any fibroblast that is derived from the neural crest.") -AnnotationAssertion( "fibroblast neural crest derived") -AnnotationAssertion(rdfs:label "neural crest derived fibroblast") +AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-5208-3432") "Any fibroblast that is deriived from the neural crest.") +AnnotationAssertion(rdfs:label "fibroblast neural crest derived") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuronal receptor cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.") -AnnotationAssertion(Annotation( ) "ZFA:0009001") AnnotationAssertion( "neuronal receptor cell (sensu Animalia)") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuronal receptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) # Class: (early embryonic cell (metazoa)) AnnotationAssertion(Annotation( "GOC:tfm") "A cell found in the embryo before the formation of all the gem layers is complete.") -AnnotationAssertion(Annotation( ) "ZFA:0009002") AnnotationAssertion(rdfs:label "early embryonic cell (metazoa)") SubClassOf( ) # Class: (migratory cranial neural crest cell) AnnotationAssertion(Annotation( "ZFA:0007091") Annotation( "https://orcid.org/0000-0001-5208-3432") "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.") -AnnotationAssertion(Annotation( ) "ZFA:0007091") AnnotationAssertion(rdfs:label "migratory cranial neural crest cell") SubClassOf( ) # Class: (migratory trunk neural crest cell) AnnotationAssertion(Annotation( "ZFA:0007095") Annotation( "https://orcid.org/0000-0001-5208-3432") "Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination.") -AnnotationAssertion(Annotation( ) "ZFA:0007095") AnnotationAssertion(rdfs:label "migratory trunk neural crest cell") SubClassOf( ) # Class: (germ line stem cell) AnnotationAssertion(Annotation( "doi:10.1016/j.stem.2012.05.016") "A stem cell that is the precursor of gametes.") -AnnotationAssertion(Annotation( ) "FBbt:00004861") -AnnotationAssertion(Annotation( ) "ZFA:0005956") +AnnotationAssertion( "FBbt:00004861") AnnotationAssertion( "germline stem cell") AnnotationAssertion(rdfs:label "germ line stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (female germ cell) @@ -15000,12 +16068,11 @@ AnnotationAssertion( "female germ cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (female germ line stem cell) AnnotationAssertion(Annotation( "doi:10.1016/j.stem.2012.05.016") "A stem cell that is the precursor of female gametes.") -AnnotationAssertion(Annotation( ) "FBbt:00004873") +AnnotationAssertion( "FBbt:00004873") AnnotationAssertion(rdfs:label "female germ line stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -15016,17 +16083,14 @@ SubClassOf(Annotation( AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") "A female germ cell that has entered meiosis.") AnnotationAssertion( "BTO:0000964") AnnotationAssertion( "CALOHA:TS-0711") -AnnotationAssertion(Annotation( ) "FBbt:00004886") +AnnotationAssertion( "FBbt:00004886") AnnotationAssertion( "FMA:18644") AnnotationAssertion( "MESH:D009865") AnnotationAssertion( "WBbt:0006797") -AnnotationAssertion(Annotation( ) "ZFA:0001109") AnnotationAssertion( "oogonium") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "oocyte") -SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -15034,14 +16098,11 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "ISBN:0721662544") "An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.") AnnotationAssertion( "FMA:83673") -AnnotationAssertion(Annotation( ) "ZFA:0005878") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "oogonial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (egg cell) @@ -15049,15 +16110,13 @@ AnnotationAssertion(Annotation( "BTO:0000369") AnnotationAssertion( "BTO:0003801") AnnotationAssertion( "CALOHA:TS-2191") -AnnotationAssertion(Annotation( ) "FBbt:00057012") +AnnotationAssertion( "FBbt:00057012") AnnotationAssertion( "FMA:67343") AnnotationAssertion( "MESH:D010063") -AnnotationAssertion(Annotation( ) "ZFA:0001570") AnnotationAssertion( "mature oocyte") AnnotationAssertion( "ovum") AnnotationAssertion(rdfs:label "egg cell") AnnotationAssertion( "https://www.swissbiopics.org/api/image/Egg_cell.svg"^^xsd:anyURI) -SubClassOf( ) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -15072,21 +16131,16 @@ SubClassOf( ObjectSomeValuesFrom( (neural crest derived neuron) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any neuron that develops from some migratory neural crest cell.") -AnnotationAssertion(Annotation( ) "ZFA:0009009") AnnotationAssertion( "neuron neural crest derived") AnnotationAssertion(rdfs:label "neural crest derived neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (glioblast) -AnnotationAssertion(Annotation( ) "ZFA:0009010") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "glioblast") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -15095,12 +16149,10 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:NV") Annotation( "http://en.wikipedia.org/wiki/Neuroblast") "A cell that will develop into a neuron often after a migration phase.") AnnotationAssertion( "BTO:0000930") AnnotationAssertion( "FMA:70563") -AnnotationAssertion(Annotation( ) "ZFA:0009011") AnnotationAssertion( "neuroblast") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuroblast (sensu Vertebrata)") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (stem cell) @@ -15109,7 +16161,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "CALOHA:TS-2086") AnnotationAssertion( "FMA:63368") -AnnotationAssertion(Annotation( ) "ZFA:0005957") AnnotationAssertion( "animal stem cell") AnnotationAssertion( ) AnnotationAssertion( ) @@ -15117,21 +16168,18 @@ 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( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (single fate stem cell) AnnotationAssertion(Annotation( "GOC:tfm") "A stem cell that self-renews as well as give rise to a single mature cell type.") AnnotationAssertion( "FMA:70569") -AnnotationAssertion(Annotation( ) "ZFA:0009013") AnnotationAssertion( "unipotent stem cell") AnnotationAssertion( "unipotential stem cell") AnnotationAssertion(rdfs:label "single fate stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (hematopoietic stem cell) @@ -15142,7 +16190,6 @@ AnnotationAssertion( "FMA:86475") AnnotationAssertion( "MESH:D006412") AnnotationAssertion( "VHOG:0001485") -AnnotationAssertion(Annotation( ) "ZFA:0009014") AnnotationAssertion( "blood forming stem cell") AnnotationAssertion( "hemopoietic stem cell") AnnotationAssertion(Annotation( ) "HSC") @@ -15153,29 +16200,14 @@ AnnotationAssertion( "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.") AnnotationAssertion(rdfs:label "hematopoietic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf(Annotation( "true") ) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (erythroid progenitor cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0721601464") "A progenitor cell committed to the erythroid lineage.") AnnotationAssertion( "BTO:0004911") -AnnotationAssertion(Annotation( ) "ZFA:0009015") AnnotationAssertion(Annotation( ) "BFU-E") AnnotationAssertion(Annotation( ) "CFU-E") AnnotationAssertion( "blast forming unit erythroid") @@ -15192,7 +16224,6 @@ SubClassOf( ObjectSomeValuesFrom( (germ line cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.") -AnnotationAssertion(Annotation( ) "ZFA:0009016") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Originally this term had some plant germ line cell children.") @@ -15204,22 +16235,18 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:add") "A stem cell that can give rise to multiple lineages of cells.") AnnotationAssertion( "FMA:84789") -AnnotationAssertion(Annotation( ) "ZFA:0009020") AnnotationAssertion( "multi-fate stem cell") AnnotationAssertion( "multifate stem cell") AnnotationAssertion( "multipotent cell") AnnotationAssertion( "multipotent stem cell") AnnotationAssertion(rdfs:label "multi fate stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (common myeloid progenitor) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0878932437") Annotation( "MESH:D023461") "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0004730") -AnnotationAssertion(Annotation( ) "ZFA:0009021") AnnotationAssertion( "common myeloid precursor") AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-GEMM") AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-S") @@ -15240,7 +16267,6 @@ DisjointClasses( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "MESH:D055015") Annotation( "PMID:16647566") Annotation( "http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell") "A progenitor cell committed to the megakaryocyte and erythroid lineages.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "ZFA:0009022") AnnotationAssertion( "CFU-EM") AnnotationAssertion( "CFU-MegE") AnnotationAssertion( "MEP") @@ -15253,17 +16279,13 @@ AnnotationAssertion( "MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.") AnnotationAssertion(rdfs:label "megakaryocyte-erythroid progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (common lymphoid progenitor) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "PMID:10407577") Annotation( "PMID:16551251") "A oligopotent progenitor cell committed to the lymphoid lineage.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "ZFA:0009023") AnnotationAssertion( "common lymphocyte precursor") AnnotationAssertion( "common lymphocyte progenitor") AnnotationAssertion( "common lymphoid precursor") @@ -15279,15 +16301,12 @@ AnnotationAssertion(rdfs:comment "CL AnnotationAssertion(rdfs:label "common lymphoid progenitor") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (totipotent stem cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:tfm") "A stem cell from which all cells of the body can form.") AnnotationAssertion( "FMA:84790") AnnotationAssertion( "MESH:D039901") -AnnotationAssertion(Annotation( ) "ZFA:0009024") AnnotationAssertion( "totipotential stem cell") AnnotationAssertion(rdfs:label "totipotent stem cell") SubClassOf( ) @@ -15301,17 +16320,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "define using PATO mulit-potent or oligopotent?") AnnotationAssertion(rdfs:label "non-terminally differentiated cell") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myoblast) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "MESH:D032446") Annotation( "PMID:21849021") "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.") AnnotationAssertion( "BTO:0000222") AnnotationAssertion( "CALOHA:TS-0650") -AnnotationAssertion(Annotation( ) "FBbt:00005083") +AnnotationAssertion( "FBbt:00005083") AnnotationAssertion( "FMA:70335") AnnotationAssertion( "VHOG:0001529") -AnnotationAssertion(Annotation( ) "ZFA:0009025") AnnotationAssertion(rdfs:label "myoblast") SubClassOf( ) @@ -15324,13 +16343,11 @@ AnnotationAssertion( "FMA:63877") AnnotationAssertion( "NCIT:C12482") AnnotationAssertion( "VHOG:0001482") -AnnotationAssertion(Annotation( ) "ZFA:0009026") AnnotationAssertion( ) AnnotationAssertion( ) 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( )) @@ -15339,10 +16356,8 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "GO_REF:0000034") Annotation( "ISBN:0618947256") "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell.") AnnotationAssertion( "BTO:0003607") AnnotationAssertion( "FMA:66783") -AnnotationAssertion(Annotation( ) "ZFA:0009027") AnnotationAssertion( "chrondoplast") AnnotationAssertion(rdfs:label "chondroblast") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -15353,12 +16368,9 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "A cell that has a filiform extrusion of the cell surface.") AnnotationAssertion( "VHOG:0001532") AnnotationAssertion( "XAO:0000031") -AnnotationAssertion(Annotation( ) "ZFA:0009032") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ciliated cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell) @@ -15367,10 +16379,9 @@ AnnotationAssertion( "BTO:0000414") AnnotationAssertion( "CALOHA:TS-2026") AnnotationAssertion( "CARO:0000077") -AnnotationAssertion(Annotation( ) "FBbt:00000124") +AnnotationAssertion( "FBbt:00000124") AnnotationAssertion( "FMA:66768") AnnotationAssertion( "WBbt:0003672") -AnnotationAssertion(Annotation( ) "ZFA:0009034") AnnotationAssertion( "epitheliocyte") AnnotationAssertion( ) AnnotationAssertion( ) @@ -15385,28 +16396,22 @@ DisjointClasses( "GOC:tfm") "An epithelial cell that has a cilia.") AnnotationAssertion( "FMA:70605") -AnnotationAssertion(Annotation( ) "ZFA:0009035") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ciliated epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (duct epithelial cell) AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-5208-3432") "An epithelial cell that is part of a duct.") -AnnotationAssertion(Annotation( ) "ZFA:0009372") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duct epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vessel endothelial cell) AnnotationAssertion(Annotation( "GOC:tfm") "An endothelial cell that lines the vasculature.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "ZFA:0009036") AnnotationAssertion( "cuboidal endothelial cell of vascular tree") AnnotationAssertion( ) AnnotationAssertion( ) @@ -15414,14 +16419,12 @@ AnnotationAssertion(rdfs:label "bloo EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (columnar/cuboidal epithelial cell) AnnotationAssertion(Annotation( "GO:0002065") Annotation( "https://orcid.org/0000-0001-5208-3432") "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "ZFA:0009038") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "columnar/cuboidal epithelial cell") @@ -15430,7 +16433,6 @@ SubClassOf( (squamous epithelial cell) AnnotationAssertion( "CALOHA:TS-1249") -AnnotationAssertion(Annotation( ) "ZFA:0009039") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "squamous epithelial cell") SubClassOf( ) @@ -15440,36 +16442,30 @@ SubClassOf( "GOC:tfm") Annotation( "ISBN:0721662544") "A flattened epithelial cell of mesenchymal origin that lines the serous cavity.") AnnotationAssertion( ) AnnotationAssertion( "FMA:66773") -AnnotationAssertion(Annotation( ) "ZFA:0009040") AnnotationAssertion( "mesotheliocyte") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell") SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (circulating cell) AnnotationAssertion(Annotation( "GOC:add") "A cell which moves among different tissues of the body, via blood, lymph, or other medium.") -AnnotationAssertion(Annotation( ) "ZFA:0009043") AnnotationAssertion(rdfs:label "circulating cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:tfm") "A cell found predominately in the blood.") AnnotationAssertion( "FMA:62844") AnnotationAssertion( "MESH:D001773") -AnnotationAssertion(Annotation( ) "ZFA:0009044") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of lung) @@ -15479,14 +16475,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuron associated cell) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuron associated cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -15495,11 +16489,9 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "ISBN:0517223651") Annotation( "ISBN:0721662544") "A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells.") AnnotationAssertion( "neuroepithelial cell") AnnotationAssertion( "BTO:0004301") -AnnotationAssertion(Annotation( ) "ZFA:0009050") AnnotationAssertion(rdfs:comment "The term \"neuroepithelial cell\" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710).") AnnotationAssertion(rdfs:label "sensory epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) # Class: (interneuron) @@ -15507,10 +16499,9 @@ SubClassOf( "GOC:tfm") Annotation( "MESH:D007395") "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0003811") -AnnotationAssertion(Annotation( ) "FBbt:00005125") +AnnotationAssertion( "FBbt:00005125") AnnotationAssertion( "FMA:67313") AnnotationAssertion( "WBbt:0005113") -AnnotationAssertion(Annotation( ) "ZFA:0009051") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "interneuron") @@ -15521,10 +16512,9 @@ SubClassOf( "MESH:D009046") Annotation( "PMID:16875686") "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0000312") -AnnotationAssertion(Annotation( ) "FBbt:00005123") +AnnotationAssertion( "FBbt:00005123") AnnotationAssertion( "FMA:83617") AnnotationAssertion( "WBbt:0005409") -AnnotationAssertion(Annotation( ) "ZFA:0009052") AnnotationAssertion( "motoneuron") AnnotationAssertion( ) AnnotationAssertion( ) @@ -15534,66 +16524,50 @@ SubClassOf( (sensory neuron) AnnotationAssertion(Annotation( "ISBN:0721662544") "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0001037") -AnnotationAssertion(Annotation( ) "FBbt:00005124") +AnnotationAssertion( "FBbt:00005124") AnnotationAssertion( "FMA:84649") AnnotationAssertion( "MESH:D011984") AnnotationAssertion( "WBbt:0005759") -AnnotationAssertion(Annotation( ) "ZFA:0009053") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "sensory neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (bipolar neuron) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0444009442") "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.") AnnotationAssertion( "FMA:67282") -AnnotationAssertion(Annotation( ) "ZFA:0009055") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bipolar neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (multipolar neuron) AnnotationAssertion(Annotation( "FMA:67287") Annotation( "GOC:tfm") "A neuron with three or more neurites, usually an axon and multiple dendrites.") AnnotationAssertion( "FMA:67287") -AnnotationAssertion(Annotation( ) "ZFA:0009056") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "multipolar neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (autonomic neuron) AnnotationAssertion(Annotation( "GOC:tfm") "A neuron whose cell body is within an autonomic ganglion.") AnnotationAssertion( "FMA:80121") -AnnotationAssertion(Annotation( ) "ZFA:0009059") AnnotationAssertion(rdfs:label "autonomic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (cholinergic neuron) AnnotationAssertion(Annotation( "GOC:tfm") "A neuron that uses acetylcholine as a vesicular neurotransmitter.") AnnotationAssertion( "BTO:0004902") -AnnotationAssertion(Annotation( ) "FBbt:00007173") +AnnotationAssertion( "FBbt:00007173") AnnotationAssertion( "FMA:84796") AnnotationAssertion( "MESH:D059329") AnnotationAssertion( "WBbt:0006840") -AnnotationAssertion(Annotation( ) "ZFA:0009060") AnnotationAssertion(rdfs:label "cholinergic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell) @@ -15602,7 +16576,6 @@ AnnotationAssertion( "BTO:0001176") AnnotationAssertion( "CALOHA:TS-0278") AnnotationAssertion( "FMA:66772") -AnnotationAssertion(Annotation( ) "ZFA:0009065") AnnotationAssertion( "endotheliocyte") AnnotationAssertion( ) AnnotationAssertion( ) @@ -15613,9 +16586,7 @@ SubClassOf( (CNS neuron (sensu Vertebrata)) -AnnotationAssertion(Annotation( ) "ZFA:0009067") AnnotationAssertion(rdfs:label "CNS neuron (sensu Vertebrata)") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -15624,38 +16595,30 @@ SubClassOf( ObjectSomeValuesFrom( "ISBN:9780123973481") "A neuron that has dendritic processes radiating from the cell body forming a star-like shape.") AnnotationAssertion( "BTO:0002316") -AnnotationAssertion(Annotation( ) "ZFA:0009072") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stellate neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuron associated cell (sensu Vertebrata)) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neuron associated cell (sensu Vertebrata)") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (glial cell) AnnotationAssertion(Annotation( "MESH:D009457") "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0002606") AnnotationAssertion( "CALOHA:TS-0415") -AnnotationAssertion(Annotation( ) "FBbt:00005144") +AnnotationAssertion( "FBbt:00005144") AnnotationAssertion( "FMA:54536") -AnnotationAssertion(Annotation( ) "ZFA:0009073") AnnotationAssertion( "neuroglial cell") AnnotationAssertion( "neuroglia") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571") AnnotationAssertion(rdfs:label "glial cell") SubClassOf( ) @@ -15666,7 +16629,6 @@ AnnotationAssertion(Annotation( "BTO:0000771") AnnotationAssertion( "CALOHA:TS-2027") AnnotationAssertion( "FMA:54538") -AnnotationAssertion(Annotation( ) "ZFA:0009074") AnnotationAssertion( "macrogliocyte") AnnotationAssertion(Annotation( "doi:10.1152/physrev.2001.81.2.871") Annotation( ) "macroglia") AnnotationAssertion( ) @@ -15681,7 +16643,6 @@ AnnotationAssertion( "BTO:0000962") AnnotationAssertion( "CALOHA:TS-0709") AnnotationAssertion( "FMA:54540") -AnnotationAssertion(Annotation( ) "ZFA:0009076") AnnotationAssertion(Annotation( "PMID:8734446") "OLs") AnnotationAssertion( "oligodendroglia") AnnotationAssertion( ) @@ -15689,14 +16650,13 @@ AnnotationAssertion( "Oligodendrocytes are reportedly MDP-positive and CD4-negative.") AnnotationAssertion(rdfs:label "oligodendrocyte") SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neurectodermal cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:068340007X") "Ectoderm destined to be nervous tissue.") -AnnotationAssertion(Annotation( ) "ZFA:0009080") AnnotationAssertion( "neurectoderm cell") AnnotationAssertion(rdfs:label "neurectodermal cell") SubClassOf( ) @@ -15707,7 +16667,6 @@ AnnotationAssertion(Annotation( "BTO:0002625") AnnotationAssertion( "BTO:0003298") AnnotationAssertion( "FMA:70546") -AnnotationAssertion(Annotation( ) "ZFA:0009081") AnnotationAssertion( "bone marrow stromal cells") AnnotationAssertion( "colony-forming unit-fibroblast") AnnotationAssertion(Annotation( "PMID:11378515") "marrow stromal cells") @@ -15734,14 +16693,12 @@ AnnotationAssertion( "BTO:0000443") AnnotationAssertion( "CALOHA:TS-0012") AnnotationAssertion( "FMA:63880") -AnnotationAssertion(Annotation( ) "ZFA:0009082") AnnotationAssertion( "adipose cell") AnnotationAssertion( "fat cell") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "adipocyte") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -15752,12 +16709,12 @@ AnnotationAssertion(Annotation( "BTO:0000249") AnnotationAssertion( "CALOHA:TS-0138") AnnotationAssertion( "FMA:66782") -AnnotationAssertion(Annotation( ) "ZFA:0009084") AnnotationAssertion( "cartilage cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chondrocyte") SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -15765,7 +16722,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") "A pigment cell is a cell that contains pigment granules.") AnnotationAssertion( "VHOG:0001678") -AnnotationAssertion(Annotation( ) "ZFA:0009090") AnnotationAssertion( "chromatocyte") AnnotationAssertion( "chromatophore") AnnotationAssertion(rdfs:label "pigment cell") @@ -15796,24 +16752,19 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "secretory cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (exocrine cell) AnnotationAssertion(Annotation( "ISBN:0198547684") "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.") AnnotationAssertion( "FMA:16014") -AnnotationAssertion(Annotation( ) "ZFA:0009092") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "exocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (glycosaminoglycan secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") "A cell that secretes glycosaminoglycans.") -AnnotationAssertion(Annotation( ) "ZFA:0009093") AnnotationAssertion( "GAG secreting cell") AnnotationAssertion( "hyaluronic acid secreting cell") AnnotationAssertion(rdfs:label "glycosaminoglycan secreting cell") @@ -15822,11 +16773,8 @@ SubClassOf( (protein secreting cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is capable of some protein secretion.") AnnotationAssertion(rdfs:label "protein secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (seromucus secreting cell) @@ -15838,16 +16786,13 @@ SubClassOf( "MESH:D055098") "A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.") AnnotationAssertion( ) AnnotationAssertion( "FMA:83809") -AnnotationAssertion(Annotation( ) "ZFA:0009096") AnnotationAssertion( "endocrinocyte") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (enteroendocrine cell) @@ -15855,7 +16800,6 @@ AnnotationAssertion(Annotation( "BTO:0003865") AnnotationAssertion( "FMA:62930") AnnotationAssertion( "MESH:D019858") -AnnotationAssertion(Annotation( ) "ZFA:0009097") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enteroendocrine cell") SubClassOf( ) @@ -15866,9 +16810,8 @@ SubClassOf( "MESH:D055099") "A neuron that is capable of some hormone secretion in response to neuronal signals.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0002691") -AnnotationAssertion(Annotation( ) "FBbt:00005130") +AnnotationAssertion( "FBbt:00005130") AnnotationAssertion( "FMA:83810") -AnnotationAssertion(Annotation( ) "ZFA:0009098") AnnotationAssertion( "neurosecretory cell") AnnotationAssertion( "neurosecretory neuron") AnnotationAssertion( ) @@ -15879,46 +16822,32 @@ The modern definition of neurosecretion has evolved to include the release of an AnnotationAssertion(rdfs:label "neuroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) # Class: (peptide hormone secreting cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is capable of some peptide hormone secretion.") -AnnotationAssertion(Annotation( ) "ZFA:0009100") AnnotationAssertion(rdfs:label "peptide hormone secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (glucagon secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") "A cell that secretes glucagon.") AnnotationAssertion( "FMA:84045") -AnnotationAssertion(Annotation( ) "ZFA:0009103") AnnotationAssertion( "glucagon-secreting cell") AnnotationAssertion(rdfs:label "glucagon secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatostatin secreting cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is capable of some somatostatin secretion.") -AnnotationAssertion(Annotation( ) "ZFA:0009105") AnnotationAssertion(rdfs:label "somatostatin secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (steroid hormone secreting cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is capable of some steroid hormone secretion.") -AnnotationAssertion(Annotation( ) "ZFA:0009106") AnnotationAssertion(rdfs:label "steroid hormone secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (contractile cell) @@ -15933,16 +16862,14 @@ AnnotationAssertion(Annotation( "BTO:0000888") AnnotationAssertion( "BTO:0000902") AnnotationAssertion( "CALOHA:TS-2032") -AnnotationAssertion(Annotation( ) "FBbt:00005074") +AnnotationAssertion( "FBbt:00005074") AnnotationAssertion( "FMA:67328") AnnotationAssertion( "WBbt:0003675") -AnnotationAssertion(Annotation( ) "ZFA:0009114") AnnotationAssertion( "muscle fiber") AnnotationAssertion( "myocyte") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle cell") AnnotationAssertion( "https://www.swissbiopics.org/api/image/Muscle_cells.svg"^^xsd:anyURI) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -15954,15 +16881,12 @@ AnnotationAssertion( "BTO:0004392") AnnotationAssertion( "CALOHA:TS-2158") AnnotationAssertion( "FMA:9727") -AnnotationAssertion(Annotation( ) "ZFA:0009115") AnnotationAssertion( "skeletal muscle cell") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell of skeletal muscle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell) @@ -15972,7 +16896,6 @@ AnnotationAssertion( "BTO:0004576") AnnotationAssertion( "CALOHA:TS-2159") AnnotationAssertion( "FMA:14072") -AnnotationAssertion(Annotation( ) "ZFA:0009118") AnnotationAssertion(Annotation( "PMID:9315361") "SMCs") AnnotationAssertion(Annotation( "MESH:D032389") "myocytes, smooth muscle") AnnotationAssertion( "smooth muscle fiber") @@ -15991,59 +16914,45 @@ AnnotationAssertion( "receptor cell") AnnotationAssertion(rdfs:label "sensory receptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (chemoreceptor cell) AnnotationAssertion(Annotation( "MESH:D002628") "A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood.") -AnnotationAssertion(Annotation( ) "ZFA:0009124") AnnotationAssertion(rdfs:label "chemoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (taste receptor cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0618947256") "A specialized cell involved in gustatory sensory perception.") AnnotationAssertion( "FMA:67910") -AnnotationAssertion(Annotation( ) "ZFA:0009126") AnnotationAssertion( "taste bud cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "taste receptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (photoreceptor cell) AnnotationAssertion(Annotation( "MESH:D010786") "A cell specialized to detect and transduce light.") AnnotationAssertion( "BTO:0001060") AnnotationAssertion( "CALOHA:TS-0868") -AnnotationAssertion(Annotation( ) "FBbt:00004211") AnnotationAssertion( "FMA:86740") -AnnotationAssertion(Annotation( ) "ZFA:0009127") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "photoreceptor cell") AnnotationAssertion( "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (electrically active cell) AnnotationAssertion(Annotation( "FB:ma") "A cell whose function is determined by the generation or the reception of an electric signal.") -AnnotationAssertion(Annotation( ) "ZFA:0009128") AnnotationAssertion(rdfs:label "electrically active cell") SubClassOf( ) # Class: (lining cell) AnnotationAssertion(Annotation( "JB:jb") "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.") -AnnotationAssertion(Annotation( ) "ZFA:0009130") AnnotationAssertion( "boundary cell") AnnotationAssertion(rdfs:label "lining cell") SubClassOf( ) @@ -16052,7 +16961,6 @@ SubClassOf( "A cell located in the synovial joint.") AnnotationAssertion( "CALOHA:TS-0995") -AnnotationAssertion(Annotation( ) "ZFA:0009131") AnnotationAssertion( "synoviocyte") AnnotationAssertion(rdfs:label "synovial cell") SubClassOf( ) @@ -16062,13 +16970,11 @@ SubClassOf( ObjectSomeValuesFrom( (barrier cell) AnnotationAssertion(Annotation( "JB:jb") "A cell whose primary function is to prevent the transport of stuff across compartments.") -AnnotationAssertion(Annotation( ) "ZFA:0009132") AnnotationAssertion(rdfs:label "barrier cell") SubClassOf( ) # Class: (insulating cell) -AnnotationAssertion(Annotation( ) "ZFA:0009134") AnnotationAssertion(rdfs:label "insulating cell") SubClassOf( ) @@ -16079,28 +16985,23 @@ AnnotationAssertion( "peripheral neuroglial cell") AnnotationAssertion( "CALOHA:TS-0898") AnnotationAssertion( "FMA:62121") -AnnotationAssertion(Annotation( ) "ZFA:0009135") AnnotationAssertion( "neurilemmal cell") AnnotationAssertion(rdfs:label "myelinating Schwann cell") SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (motile cell) AnnotationAssertion(Annotation( "FB:ma") "A cell that moves by its own activities.") -AnnotationAssertion(Annotation( ) "ZFA:0009136") AnnotationAssertion(rdfs:label "motile cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (ectodermal cell) AnnotationAssertion(Annotation( "MESH:D004475") "A cell of the outer of the three germ layers of the embryo.") AnnotationAssertion( "FMA:72549") -AnnotationAssertion(Annotation( ) "ZFA:0009137") AnnotationAssertion( "ectoderm cell") AnnotationAssertion(rdfs:label "ectodermal cell") SubClassOf( ) @@ -16110,7 +17011,6 @@ SubClassOf( ObjectSomeValuesFrom( "MESH:D008648") "A cell of the middle germ layer of the embryo.") AnnotationAssertion( "FMA:72554") -AnnotationAssertion(Annotation( ) "ZFA:0009138") AnnotationAssertion( "mesoblast") AnnotationAssertion( "mesoderm cell") AnnotationAssertion( ) @@ -16122,7 +17022,6 @@ SubClassOf( ObjectSomeValuesFrom( "MESH:D004707") "A cell of the inner of the three germ layers of the embryo.") AnnotationAssertion( "FMA:72555") -AnnotationAssertion(Annotation( ) "ZFA:0009139") AnnotationAssertion( "endoderm cell") AnnotationAssertion(rdfs:label "endodermal cell") SubClassOf( ) @@ -16135,8 +17034,6 @@ AnnotationAssertion( "non-nucleated cell") AnnotationAssertion(rdfs:label "anucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (single nucleate cell) @@ -16144,16 +17041,11 @@ DisjointClasses( "FB:ma") Annotation( "GOC:tfm") "A cell with a single nucleus.") AnnotationAssertion(rdfs:label "single nucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -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) @@ -16165,8 +17057,6 @@ AnnotationAssertion( "syncytium") AnnotationAssertion(rdfs:label "multinucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (erythrocyte) @@ -16182,49 +17072,35 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (eukaryotic cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that only exists in Eukaryota.") AnnotationAssertion( "MESH:D005057") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eukaryotic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (Eumycetozoan cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that only exists in Eumycetozoa.") AnnotationAssertion(rdfs:label "Eumycetozoan cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (eye photoreceptor cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any photoreceptor cell that is part of some eye.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "ZFA:0009154") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "eye photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (structural cell) AnnotationAssertion(Annotation( "TAIR:sr") "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.") -AnnotationAssertion(Annotation( ) "ZFA:0005745") AnnotationAssertion(rdfs:label "structural cell") SubClassOf( ) @@ -16232,16 +17108,13 @@ SubClassOf( "GOC:tfm") Annotation( "ISBN:0721662544") "A mature sexual reproductive cell having a single set of unpaired chromosomes.") AnnotationAssertion( "CALOHA:TS-0395") -AnnotationAssertion(Annotation( ) "FBbt:00005412") +AnnotationAssertion( "FBbt:00005412") AnnotationAssertion( "FMA:18649") -AnnotationAssertion(Annotation( ) "ZFA:0009156") AnnotationAssertion( "haploid nucleated cell") AnnotationAssertion( "haploid germ cell") AnnotationAssertion(rdfs:label "gamete") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (crystallin accumulating cell) @@ -16269,34 +17142,27 @@ SubClassOf( (extracellular matrix secreting cell) -AnnotationAssertion(Annotation( ) "ZFA:0009162") AnnotationAssertion(rdfs:label "extracellular matrix secreting cell") SubClassOf( ) # Class: (oxygen accumulating cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that is capable of some oxygen transport.") -AnnotationAssertion(Annotation( ) "ZFA:0009164") AnnotationAssertion(rdfs:label "oxygen accumulating cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (migratory neural crest cell) AnnotationAssertion(Annotation( "doi:10.1016/j.stem.2015.02.017") "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.") AnnotationAssertion( "FMA:86667") -AnnotationAssertion(Annotation( ) "ZFA:0007086") AnnotationAssertion(rdfs:label "migratory neural crest cell") +SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchyme condensation cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:5025404") "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.") -AnnotationAssertion(Annotation( ) "ZFA:0009166") AnnotationAssertion(rdfs:label "mesenchyme condensation cell") SubClassOf( ) @@ -16304,46 +17170,33 @@ SubClassOf( "GOC:tfm") Annotation( "ISBN:0618947256") "An early neural cell developing from the early ependymal cell of the neural tube.") AnnotationAssertion( "FMA:70564") -AnnotationAssertion(Annotation( ) "ZFA:0009169") AnnotationAssertion( "spongioblast") AnnotationAssertion(rdfs:label "glioblast (sensu Vertebrata)") SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (scleral cell) AnnotationAssertion(Annotation( "GOC:add") "A cell of the sclera of the eye.") -AnnotationAssertion(Annotation( ) "ZFA:0009174") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "scleral cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (choroidal cell of the eye) AnnotationAssertion(Annotation( "GOC:add") "A structural cell that is part of optic choroid.") -AnnotationAssertion(Annotation( ) "ZFA:0009175") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "choroidal cell of the eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (extraembryonic cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that is part of some extraembryonic structure.") -AnnotationAssertion(Annotation( ) "ZFA:0009176") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "extraembryonic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (trophoblast cell) @@ -16365,7 +17218,6 @@ SubClassOf( "MESH:D001756") "An undifferentiated cell produced by early cleavages of the fertilized egg (zygote).") AnnotationAssertion( "BTO:0001473") AnnotationAssertion( "FMA:72551") -AnnotationAssertion(Annotation( ) "ZFA:0009177") AnnotationAssertion( "blastomere") AnnotationAssertion(rdfs:label "blastoderm cell") SubClassOf( ) @@ -16374,18 +17226,15 @@ SubClassOf( "PMID:18282570") "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell.") AnnotationAssertion( "FMA:86767") -AnnotationAssertion(Annotation( ) "ZFA:0009179") AnnotationAssertion(rdfs:comment "Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo.") AnnotationAssertion(rdfs:label "multi-potent skeletal muscle stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (vascular associated smooth muscle cell) AnnotationAssertion(Annotation( "GOC:dsd") Annotation( "GOC:tfm") "A smooth muscle cell associated with the vasculature.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "ZFA:0009181") AnnotationAssertion( "VSMC") AnnotationAssertion( "vascular smooth muscle cell") AnnotationAssertion( ) @@ -16394,7 +17243,6 @@ AnnotationAssertion(rdfs:label "vasc EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (epidermal cell) @@ -16403,14 +17251,12 @@ AnnotationAssertion( "CALOHA:TS-0283") AnnotationAssertion( "FMA:62411") AnnotationAssertion( "MESH:D000078404") -AnnotationAssertion(Annotation( ) "ZFA:0009183") AnnotationAssertion(Annotation( "FMA:62411") "cell of epidermis") AnnotationAssertion(Annotation( "FMA:62411") "epithelial cell of skin") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epidermal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (animal zygote) @@ -16422,42 +17268,33 @@ AnnotationAssertion( "animal zygote") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (electrically responsive cell) AnnotationAssertion(Annotation( "FB:ma") "A cell whose function is determined by its response to an electric signal.") -AnnotationAssertion(Annotation( ) "ZFA:0009190") AnnotationAssertion(rdfs:label "electrically responsive cell") SubClassOf( ) # Class: (ganglion interneuron) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any interneuron that has its soma located in some ganglion.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ganglion interneuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (CNS interneuron) AnnotationAssertion(Annotation( "doi:10.1016/B978-0-12-817424-1.00001-X") "An interneuron that has its cell body in a central nervous system.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( ) "ZFA:0009191") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system.") AnnotationAssertion(rdfs:label "CNS interneuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (electrically signaling cell) AnnotationAssertion(Annotation( "FB:ma") "A cell that initiates an electrical signal and passes that signal to another cell.") -AnnotationAssertion(Annotation( ) "ZFA:0009193") AnnotationAssertion(rdfs:label "electrically signaling cell") SubClassOf( ) @@ -16466,16 +17303,12 @@ SubClassOf( "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) Annotation( "FB:ma") Annotation( "PMID:32646579") "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label "polyploid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (haploid cell) AnnotationAssertion(Annotation( "FB:ma") Annotation( "GOC:tfm") "A cell whose nucleus contains a single haploid genome.") AnnotationAssertion(rdfs:label "haploid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (obliquely striated muscle cell) @@ -16483,8 +17316,6 @@ AnnotationAssertion(Annotation( "Examples include the somatic muscles of nemotodes and cephalopods.") AnnotationAssertion(rdfs:label "obliquely striated muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (carbohydrate secreting cell) @@ -16493,41 +17324,34 @@ SubClassOf( (biogenic amine secreting cell) -AnnotationAssertion(Annotation( ) "ZFA:0009212") AnnotationAssertion(rdfs:label "biogenic amine secreting cell") SubClassOf( ) # Class: (serotonin secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:19630576") "A cell type that secretes 5-Hydroxytryptamine (serotonin).") -AnnotationAssertion(Annotation( ) "ZFA:0009213") AnnotationAssertion( "5-HT secreting cell") AnnotationAssertion( "5-Hydroxytryptamine secreting cell") AnnotationAssertion(rdfs:label "serotonin secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (noradrenergic cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:068340007X") "A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme.") -AnnotationAssertion(Annotation( ) "ZFA:0009214") AnnotationAssertion( "noradrenaline secreting cell") AnnotationAssertion( "norepinephrin secreting cell") AnnotationAssertion( "norepinephrine secreting cell") AnnotationAssertion(rdfs:label "noradrenergic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (visible light photoreceptor cell) AnnotationAssertion(Annotation( "GOC:tfm") "A photoreceptor cell that detects visible light.") -AnnotationAssertion(Annotation( ) "ZFA:0009219") AnnotationAssertion(rdfs:label "visible light photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (stromal cell) @@ -16535,12 +17359,10 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0002064") AnnotationAssertion( "FMA:83624") -AnnotationAssertion(Annotation( ) "ZFA:0009226") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stromal cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -16548,49 +17370,37 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "MESH:D032386") "A precursor cell destined to differentiate into cardiac muscle cell.") AnnotationAssertion( "FMA:84797") -AnnotationAssertion(Annotation( ) "ZFA:0009234") AnnotationAssertion( "cardiac muscle progenitor cell") AnnotationAssertion( "cardiomyocyte progenitor cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) # Class: (smooth muscle myoblast) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "MESH:D032390") "A precursor cell destined to differentiate into smooth muscle myocytes.") AnnotationAssertion( "FMA:84798") -AnnotationAssertion(Annotation( ) "ZFA:0009235") AnnotationAssertion(Annotation( "MESH:D032390") "myoblast, smooth muscle") AnnotationAssertion( "satellite cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle myoblast) AnnotationAssertion(Annotation( "SANBI:mhl") "A myoblast that differentiates into skeletal muscle fibers.") AnnotationAssertion( "FMA:84799") -AnnotationAssertion(Annotation( ) "ZFA:0009236") AnnotationAssertion( "skeletal myoblast") AnnotationAssertion(rdfs:label "skeletal muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fungal cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that only exists in Fungi.") AnnotationAssertion(rdfs:label "fungal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (syncytiotrophoblast cell) @@ -16606,8 +17416,6 @@ AnnotationAssertion( "syncytiotrophoblast cell") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/2100") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (afferent neuron) @@ -16615,7 +17423,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "MESH:D009475") "A neuron which conveys sensory information centrally from the periphery.") AnnotationAssertion( ) AnnotationAssertion( "FMA:87653") -AnnotationAssertion(Annotation( ) "ZFA:0009238") AnnotationAssertion( "input neuron") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "afferent neuron") @@ -16624,7 +17431,6 @@ SubClassOf( (efferent neuron) AnnotationAssertion(Annotation( "MESH:D009476") "A neuron which sends impulses peripherally to activate muscles or secretory cells.") -AnnotationAssertion(Annotation( ) "ZFA:0009239") AnnotationAssertion( "output neuron") AnnotationAssertion(rdfs:label "efferent neuron") SubClassOf( ) @@ -16635,11 +17441,10 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0000938") AnnotationAssertion( "CALOHA:TS-0683") -AnnotationAssertion(Annotation( ) "FBbt:00005106") +AnnotationAssertion( "FBbt:00005106") AnnotationAssertion( "FMA:54527") AnnotationAssertion( "VHOG:0001483") AnnotationAssertion( "WBbt:0003679") -AnnotationAssertion(Annotation( ) "ZFA:0009248") AnnotationAssertion( "nerve cell") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16661,16 +17466,12 @@ AnnotationAssertion( "FMA:62863") AnnotationAssertion( "MESH:D008214") AnnotationAssertion( "VHOG:0001535") -AnnotationAssertion(Annotation( ) "ZFA:0009250") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)") AnnotationAssertion(rdfs:label "lymphocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -16685,29 +17486,12 @@ AnnotationAssertion( "proerythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (basophilic erythroblast) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721601464") "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.") AnnotationAssertion( "FMA:83505") -AnnotationAssertion(Annotation( ) "ZFA:0005236") AnnotationAssertion(Annotation( "ISBN:0721601464") "basophilic normoblast") AnnotationAssertion(Annotation( "ISBN:0721601464") "early erythroblast") AnnotationAssertion(Annotation( "ISBN:0721601464") "early normoblast") @@ -16715,15 +17499,12 @@ AnnotationAssertion(Annotation( "basophilic erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (polychromatophilic erythroblast) AnnotationAssertion(Annotation( "ISBN:0721601464") "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.") AnnotationAssertion( "FMA:83506") -AnnotationAssertion(Annotation( ) "ZFA:0005241") AnnotationAssertion(Annotation( "ISBN:0721601464") "intermediate erythroblast") AnnotationAssertion(Annotation( "ISBN:0721601464") "intermediate normoblast") AnnotationAssertion(Annotation( "ISBN:0721601464") "polychromatic erythroblast") @@ -16733,9 +17514,6 @@ AnnotationAssertion(Annotation( "polychromatophilic erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (orthochromatic erythroblast) @@ -16750,8 +17528,6 @@ AnnotationAssertion(Annotation( "orthochromatic erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (megakaryocyte progenitor cell) @@ -16777,23 +17553,8 @@ AnnotationAssertion( "Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative.") AnnotationAssertion(rdfs:label "megakaryocyte progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (megakaryocyte) @@ -16821,65 +17582,41 @@ AnnotationAssertion(Annotation( "BTO:0001173") AnnotationAssertion( "CALOHA:TS-0864") AnnotationAssertion( "MESH:D012156") -AnnotationAssertion(Annotation( ) "ZFA:0009252") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reticulocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (nucleate erythrocyte) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOc:tfm") "An erythrocyte having a nucleus.") AnnotationAssertion( "RBC") AnnotationAssertion( "red blood cell") -AnnotationAssertion(Annotation( ) "ZFA:0009256") AnnotationAssertion(rdfs:label "nucleate erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (angioblastic mesenchymal cell) AnnotationAssertion(Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "PMID:12768659") "A mesenchymal stem cell capable of developing into blood vessel endothelium.") -AnnotationAssertion(Annotation( ) "ZFA:0009258") AnnotationAssertion( "angioblast") AnnotationAssertion( "chondroplast") AnnotationAssertion(rdfs:comment "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.") AnnotationAssertion(rdfs:label "angioblastic mesenchymal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac mesenchymal cell) AnnotationAssertion(Annotation( "PMID:18816864") "A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field.") -AnnotationAssertion(Annotation( ) "ZFA:0009259") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac mesenchymal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (retinal cone cell) @@ -16888,7 +17625,6 @@ AnnotationAssertion( "BTO:0001036") AnnotationAssertion( "CALOHA:TS-0866") AnnotationAssertion( "FMA:67748") -AnnotationAssertion(Annotation( ) "ZFA:0009262") AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") "cone") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16903,16 +17639,13 @@ AnnotationAssertion( "BTO:0004298") AnnotationAssertion( "CALOHA:TS-0173") AnnotationAssertion( "FMA:70551") -AnnotationAssertion(Annotation( ) "ZFA:0009264") AnnotationAssertion(Annotation( "FMA:70551") "epithelial cell of cornea") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "corneal epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (germ cell) @@ -16929,11 +17662,8 @@ SubClassOf( ObjectSomeValuesFrom( (androgen secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") "A steroid hormone secreting cell that secretes androgen.") -AnnotationAssertion(Annotation( ) "ZFA:0009271") AnnotationAssertion(rdfs:label "androgen secreting cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (enucleate erythrocyte) @@ -16943,7 +17673,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "enucleate erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -16954,15 +17683,12 @@ AnnotationAssertion( "FMA:67310") AnnotationAssertion( "FMA:86775") AnnotationAssertion( "NIFSTD:sao862606388") -AnnotationAssertion(Annotation( ) "ZFA:0009273") AnnotationAssertion( "projection neuron") AnnotationAssertion( "pyramidal cell") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (retinal rod cell) @@ -16971,7 +17697,6 @@ AnnotationAssertion( "BTO:0001024") AnnotationAssertion( "CALOHA:TS-0870") AnnotationAssertion( "FMA:67747") -AnnotationAssertion(Annotation( ) "ZFA:0009275") AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") "rod") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16983,7 +17708,6 @@ SubClassOf( ObjectSomeValuesFrom( "FB:ma") Annotation( "GOC:tfm") "A cell whose primary function is to support other cell types.") AnnotationAssertion( "BTO:0002315") -AnnotationAssertion(Annotation( ) "ZFA:0009387") AnnotationAssertion( "supportive cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "supporting cell") @@ -16992,7 +17716,6 @@ SubClassOf( (collagen secreting cell) AnnotationAssertion(Annotation( "GOC:tfm") "An extracellular matrix secreting cell that secretes collagen.") -AnnotationAssertion(Annotation( ) "ZFA:0009287") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "collagen secreting cell") SubClassOf( ) @@ -17001,7 +17724,6 @@ SubClassOf( "GOC:tfm") Annotation( "PMID:1381289") "A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.") AnnotationAssertion( "FMA:70567") -AnnotationAssertion(Annotation( ) "ZFA:0009288") AnnotationAssertion( "gonocyte") AnnotationAssertion( "primitive germ cell") AnnotationAssertion( ) @@ -17009,7 +17731,6 @@ AnnotationAssertion(rdfs:label "prim EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (female gamete) @@ -17021,39 +17742,27 @@ SubClassOf( (muscle precursor cell) AnnotationAssertion(Annotation( "GOC:add") "A non-terminally differentiated cell that is capable of developing into a muscle cell.") -AnnotationAssertion(Annotation( ) "ZFA:0009291") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "muscle precursor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (stellate interneuron) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any interneuron that has characteristic some stellate morphology.") -AnnotationAssertion(Annotation( ) "ZFA:0009297") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stellate interneuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (neurogliaform cell) AnnotationAssertion(Annotation( "JB:jb") Annotation( "PMID:17122314") "An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts.") -AnnotationAssertion(Annotation( ) "ZFA:0009299") AnnotationAssertion(Annotation( "PMID:18568015") "NGF cell") AnnotationAssertion(Annotation( "PMID:3235828") "neuroglioform cell") AnnotationAssertion( "spiderweb cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neurogliaform cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (PP cell) @@ -17076,19 +17785,14 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "neurecto-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatic stem cell) AnnotationAssertion(Annotation( "GO:0048103") "A stem cell that can give rise to cell types of the body other than those of the germ-line.") AnnotationAssertion( "CALOHA:TS-2086") AnnotationAssertion( "MESH:D053687") -AnnotationAssertion(Annotation( ) "ZFA:0009307") AnnotationAssertion(rdfs:label "somatic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (striated muscle cell) @@ -17096,12 +17800,9 @@ AnnotationAssertion(Annotation( "BTO:0002916") AnnotationAssertion( "CALOHA:TS-2157") AnnotationAssertion( "FMA:86936") -AnnotationAssertion(Annotation( ) "ZFA:0005784") AnnotationAssertion(rdfs:label "striated muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (leukocyte) @@ -17113,7 +17814,6 @@ AnnotationAssertion( "FMA:62852") AnnotationAssertion( "MESH:D007962") AnnotationAssertion( "NCIT:C12529") -AnnotationAssertion(Annotation( ) "ZFA:0009309") AnnotationAssertion( "leucocyte") AnnotationAssertion( "white blood cell") AnnotationAssertion( "immune cell") @@ -17121,15 +17821,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "leukocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (retinal ganglion cell) @@ -17138,7 +17833,6 @@ AnnotationAssertion( "BTO:0001800") AnnotationAssertion( "FMA:67765") AnnotationAssertion( "MESH:D012165") -AnnotationAssertion(Annotation( ) "ZFA:0009310") AnnotationAssertion( "gangliocyte") AnnotationAssertion( "ganglion cell of retina") AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "RGC") @@ -17160,7 +17854,6 @@ AnnotationAssertion( "CALOHA:TS-0115") AnnotationAssertion( "FMA:14067") AnnotationAssertion( "MESH:D032383") -AnnotationAssertion(Annotation( ) "ZFA:0009316") AnnotationAssertion(Annotation( "GO:0048739") "cardiac muscle fiber") AnnotationAssertion( "cardiac myocyte") AnnotationAssertion( "cardiomyocyte") @@ -17171,10 +17864,6 @@ AnnotationAssertion( "This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction.") AnnotationAssertion(rdfs:label "cardiac muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (myeloid cell) @@ -17183,13 +17872,10 @@ AnnotationAssertion(Annotation( "BTO:0001441") AnnotationAssertion( "CALOHA:TS-0647") AnnotationAssertion( "MESH:D022423") -AnnotationAssertion(Annotation( ) "ZFA:0009324") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myeloid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (erythroid lineage cell) @@ -17198,7 +17884,6 @@ AnnotationAssertion( "CALOHA:TS-0290") AnnotationAssertion( "FMA:62845") AnnotationAssertion( "FMA:83516") -AnnotationAssertion(Annotation( ) "ZFA:0009325") AnnotationAssertion( "erythropoietic cell") AnnotationAssertion( ) AnnotationAssertion( ) @@ -17213,39 +17898,21 @@ AnnotationAssertion( "CALOHA:TS-0289") AnnotationAssertion( "FMA:83504") AnnotationAssertion( "MESH:D004900") -AnnotationAssertion(Annotation( ) "ZFA:0005237") AnnotationAssertion( "normoblast") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "erythroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (myeloid leukocyte) AnnotationAssertion(Annotation( "GOC:add") "A cell of the monocyte, granulocyte, or mast cell lineage.") -AnnotationAssertion(Annotation( ) "ZFA:0009326") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myeloid leukocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (hematopoietic multipotent progenitor cell) @@ -17253,7 +17920,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0000725") AnnotationAssertion( "CALOHA:TS-0448") -AnnotationAssertion(Annotation( ) "ZFA:0009354") AnnotationAssertion( "MPP") AnnotationAssertion( "hemopoietic progenitor cell") AnnotationAssertion( ) @@ -17262,23 +17928,8 @@ 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(Annotation( "true") ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -17289,14 +17940,11 @@ AnnotationAssertion( "BTO:0004731") AnnotationAssertion( "CALOHA:TS-2025") AnnotationAssertion( "FMA:70338") -AnnotationAssertion(Annotation( ) "ZFA:0009355") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this is a class of cell types, not an identified single cell type.") AnnotationAssertion(rdfs:label "lymphoid lineage restricted progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (myeloid lineage restricted progenitor cell) @@ -17307,15 +17955,12 @@ AnnotationAssertion( "BTO:0004730") AnnotationAssertion( "CALOHA:TS-2099") AnnotationAssertion( "FMA:70339") -AnnotationAssertion(Annotation( ) "ZFA:0009356") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this is a class of cell types, not an identified single cell type.") AnnotationAssertion(rdfs:label "myeloid lineage restricted progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mononuclear cell) @@ -17323,31 +17968,26 @@ AnnotationAssertion(Annotation( "BTO:0000878") AnnotationAssertion( "CALOHA:TS-0768") AnnotationAssertion( "FMA:86713") -AnnotationAssertion(Annotation( ) "ZFA:0009357") AnnotationAssertion( "mononuclear leukocyte") AnnotationAssertion( "peripheral blood mononuclear cell") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mononuclear cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "true") ) # Class: (serotonergic neuron) AnnotationAssertion(Annotation( "SANBI:mhl") "A neuron that releases serotonin as a neurotransmitter.") -AnnotationAssertion(Annotation( ) "FBbt:00005133") +AnnotationAssertion( "FBbt:00005133") AnnotationAssertion( "MESH:D059326") AnnotationAssertion( "WBbt:0006837") -AnnotationAssertion(Annotation( ) "ZFA:0009361") AnnotationAssertion( "5-HT neuron") AnnotationAssertion( "5-hydroxytryptamine neuron") AnnotationAssertion( "serotinergic neuron") AnnotationAssertion(rdfs:label "serotonergic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (hematopoietic cell) @@ -17356,7 +17996,6 @@ AnnotationAssertion( "CALOHA:TS-2017") AnnotationAssertion( "FMA:70366") AnnotationAssertion( "FMA:83598") -AnnotationAssertion(Annotation( ) "ZFA:0005830") AnnotationAssertion( "haematopoietic cell") AnnotationAssertion( "haemopoietic cell") AnnotationAssertion( "hemopoietic cell") @@ -17374,8 +18013,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (hematopoietic oligopotent progenitor cell, lineage-negative) @@ -17385,18 +18022,8 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "hematopoietic oligopotent progenitor cell, lineage-negative") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (abnormal cell) @@ -17409,7 +18036,6 @@ AnnotationAssertion(rdfs:comment "ht AnnotationAssertion(rdfs:label "abnormal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (neoplastic cell) @@ -17424,7 +18050,6 @@ AnnotationAssertion(rdfs:comment "ht AnnotationAssertion(rdfs:label "neoplastic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (malignant cell) @@ -17438,7 +18063,6 @@ AnnotationAssertion(rdfs:comment "ht AnnotationAssertion(rdfs:label "malignant cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (erythroid progenitor cell, mammalian) @@ -17454,19 +18078,6 @@ AnnotationAssertion( "erythroid progenitor cell, mammalian") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (hematopoietic lineage restricted progenitor cell) @@ -17476,9 +18087,8 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hematopoietic lineage restricted progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf(Annotation( "true") ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -17491,9 +18101,8 @@ 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(Annotation( "true") ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (type A enteroendocrine cell) @@ -17504,8 +18113,6 @@ AnnotationAssertion( AnnotationAssertion( "FMA:62939") AnnotationAssertion(rdfs:label "type A enteroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (Purkinje myocyte) @@ -17561,9 +18168,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-06-29T03:38:14Z") AnnotationAssertion( "FMA:69075") -AnnotationAssertion(Annotation( ) "ZFA:0009383") AnnotationAssertion(rdfs:label "endo-epithelial cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -17573,12 +18178,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-06-29T03:38:22Z") AnnotationAssertion( "FMA:69074") -AnnotationAssertion(Annotation( ) "ZFA:0009385") AnnotationAssertion(rdfs:label "ecto-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (meso-epithelial cell) @@ -17586,13 +18187,9 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-06-29T03:49:14Z") AnnotationAssertion( "FMA:69076") -AnnotationAssertion(Annotation( ) "ZFA:0009388") AnnotationAssertion( "epithelial mesenchymal cell") AnnotationAssertion(rdfs:label "meso-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (specialized cardiac myocyte) @@ -17614,7 +18211,6 @@ AnnotationAssertion( "nongranular leukocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone marrow cell) @@ -17629,7 +18225,6 @@ AnnotationAssertion(rdfs:comment "MH AnnotationAssertion(rdfs:label "bone marrow cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (hilus cell of ovary) @@ -17654,8 +18249,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "stromal cell of ovary") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell of vascular tree) @@ -17685,8 +18278,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "capillary endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) # Class: (general ecto-epithelial cell) @@ -17706,7 +18298,6 @@ AnnotationAssertion( "epithelial cell of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mucous cell of stomach) @@ -17716,8 +18307,8 @@ AnnotationAssertion( AnnotationAssertion( "FMA:63464") AnnotationAssertion(rdfs:label "mucous cell of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "true") ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (stem cell of gastric gland) @@ -17728,9 +18319,7 @@ AnnotationAssertion( "stem cell of gastric gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (vertebrate lens cell) @@ -17757,7 +18346,6 @@ AnnotationAssertion(rdfs:label "lens EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (marrow fibroblast) @@ -17768,7 +18356,6 @@ AnnotationAssertion( "marrow fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (nucleate cell) @@ -17778,8 +18365,6 @@ AnnotationAssertion( AnnotationAssertion( "FMA:67513") AnnotationAssertion(rdfs:label "nucleate cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (peripheral blood stem cell) @@ -17793,8 +18378,6 @@ AnnotationAssertion( "peripheral blood stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of alimentary canal) @@ -17804,7 +18387,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "epithelial cell of alimentary canal") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of esophagus) @@ -17812,12 +18394,10 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-09-08T09:28:20Z") AnnotationAssertion( "FMA:63071") -AnnotationAssertion(Annotation( ) "ZFA:0009400") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell of sinusoid) @@ -17830,8 +18410,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endothelial cell of sinusoid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (type A cell of stomach) @@ -17842,7 +18420,6 @@ AnnotationAssertion( "type A cell of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (epithelial cell of skin gland) @@ -17854,7 +18431,6 @@ AnnotationAssertion( "epithelial cell of skin gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural cell) @@ -17866,8 +18442,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neural cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (connective tissue cell) @@ -17877,12 +18451,9 @@ AnnotationAssertion( AnnotationAssertion( "CALOHA:TS-2096") AnnotationAssertion( "FMA:63875") AnnotationAssertion( "MESH:D003239") -AnnotationAssertion(Annotation( ) "ZFA:0009392") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "connective tissue cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic cell (metazoa)) @@ -17892,7 +18463,6 @@ AnnotationAssertion( AnnotationAssertion( "CALOHA:TS-0263") AnnotationAssertion( "FMA:82840") AnnotationAssertion( "WBbt:0007028") -AnnotationAssertion(Annotation( ) "ZFA:0007089") AnnotationAssertion(rdfs:label "embryonic cell (metazoa)") SubClassOf( ) @@ -17903,7 +18473,6 @@ AnnotationAssertion( "2010-09-20T02:25:25Z") AnnotationAssertion(rdfs:label "neural crest derived adipocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (endocardial cell) @@ -17919,8 +18488,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocardial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) # Class: (gestational hematopoietic stem cell) @@ -17930,7 +18498,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "gestational hematopoietic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (keratocyte) @@ -17945,8 +18512,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "keratocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (respiratory epithelial cell) @@ -17959,21 +18526,17 @@ AnnotationAssertion( "respiratory epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (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( ) AnnotationAssertion( "2010-09-24T01:13:01Z") -AnnotationAssertion(Annotation( ) "FBbt:00005812") +AnnotationAssertion( "FBbt:00005812") AnnotationAssertion( "myotubule") AnnotationAssertion( "single cell sarcomere") AnnotationAssertion(rdfs:label "myotube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (Schwann cell precursor) @@ -17984,7 +18547,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "Schwann cell precursor") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (immature Schwann cell) @@ -17993,7 +18555,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-09-24T02:10:31Z") AnnotationAssertion( "Schwann cell") -AnnotationAssertion(Annotation( ) "ZFA:0001725") +AnnotationAssertion( "ZFA:0001725") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "immature Schwann cell") SubClassOf( ) @@ -18007,7 +18569,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "nucleated reticulocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (enucleated reticulocyte) @@ -18019,9 +18580,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enucleated reticulocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (oligodendrocyte precursor cell) @@ -18038,9 +18597,9 @@ 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( ))) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiocyte) @@ -18055,8 +18614,6 @@ 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( ObjectSomeValuesFrom( )) # Class: (adventitial cell) @@ -18070,7 +18627,6 @@ AnnotationAssertion(rdfs:label "adve EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (subcutaneous adipocyte) @@ -18084,7 +18640,6 @@ AnnotationAssertion( "subcutaneous adipocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (aortic smooth muscle cell) @@ -18095,8 +18650,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "aortic smooth muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) # Class: (mesenchymal stem cell of the bone marrow) @@ -18105,8 +18659,6 @@ AnnotationAssertion( "2011-02-28T01:47:47Z") AnnotationAssertion(rdfs:label "mesenchymal stem cell of the bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (vein endothelial cell) @@ -18123,14 +18675,12 @@ AnnotationAssertion( "vein endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -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") -AnnotationAssertion(Annotation( ) "ZFA:0005773") AnnotationAssertion(rdfs:comment "See CL:0002619.") AnnotationAssertion(rdfs:label "embryonic blood vessel endothelial progenitor cell") SubClassOf( ) @@ -18143,7 +18693,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "fibroblast of the aortic adventitia") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of cardiac tissue) @@ -18156,17 +18705,14 @@ AnnotationAssertion(rdfs:label "fibr EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of dermis) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any skin fibroblast that is part of some dermis.") AnnotationAssertion( ) AnnotationAssertion( "2011-02-28T05:05:33Z") AnnotationAssertion(rdfs:label "fibroblast of dermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of lung) @@ -18179,7 +18725,6 @@ AnnotationAssertion( "fibroblast of lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of pulmonary artery) @@ -18191,7 +18736,6 @@ AnnotationAssertion( "fibroblast of pulmonary artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchymal stem cell of adipose tissue) @@ -18202,8 +18746,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchymal stem cell of adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (Schwann cell) @@ -18233,8 +18775,6 @@ AnnotationAssertion( "retinal blood vessel endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell of the brachiocephalic vasculature) @@ -18243,8 +18783,7 @@ AnnotationAssertion( "2011-03-06T05:00:58Z") AnnotationAssertion(rdfs:label "smooth muscle cell of the brachiocephalic vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) # Class: (smooth muscle cell of the brain vasculature) @@ -18254,8 +18793,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "smooth muscle cell of the brain vasculature") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell of the pulmonary artery) @@ -18268,8 +18805,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle cell of the pulmonary artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) # Class: (smooth muscle cell of the subclavian artery) @@ -18278,8 +18814,7 @@ AnnotationAssertion( "2011-03-06T05:01:52Z") AnnotationAssertion(rdfs:label "smooth muscle cell of the subclavian artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) # Class: (smooth muscle cell of the carotid artery) @@ -18288,8 +18823,7 @@ AnnotationAssertion( "2011-03-06T05:01:56Z") AnnotationAssertion(rdfs:label "smooth muscle cell of the carotid artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) # Class: (smooth muscle cell of the esophagus) @@ -18299,7 +18833,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "smooth muscle cell of the esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (raphe nuclei neuron) @@ -18309,8 +18842,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "raphe nuclei neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuron of the ventral spinal cord) @@ -18320,8 +18851,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "neuron of the ventral spinal cord") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (skin fibroblast) @@ -18336,18 +18865,15 @@ AnnotationAssertion( "skin fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of lower respiratory tract) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any respiratory epithelial cell that is part of some lower respiratory tract.") AnnotationAssertion( ) AnnotationAssertion( "2011-06-21T12:29:31Z") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of lower respiratory tract") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (glandular cell of esophagus) @@ -18371,7 +18897,6 @@ AnnotationAssertion( "glandular cell of stomach") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (myocardial endocrine cell of atrium) @@ -18382,7 +18907,6 @@ AnnotationAssertion( "myocardial endocrine cell of atrium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardioblast) @@ -18401,7 +18925,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2011-08-16T02:38:01Z") AnnotationAssertion(rdfs:label "retinal progenitor cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -18413,8 +18936,6 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tongue muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural crest derived neuroblast) @@ -18423,7 +18944,6 @@ AnnotationAssertion( "2011-08-22T09:24:15Z") AnnotationAssertion(rdfs:label "neural crest derived neuroblast") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bistratified retinal ganglion cell) @@ -18436,8 +18956,6 @@ AnnotationAssertion( "CL:0003001") AnnotationAssertion(rdfs:label "bistratified retinal ganglion cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (monostratified cell) @@ -18448,8 +18966,6 @@ AnnotationAssertion( "CL:0004246") AnnotationAssertion(rdfs:label "monostratified cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (bistratified cell) @@ -18459,29 +18975,22 @@ AnnotationAssertion( "CL:0004247") AnnotationAssertion(rdfs:label "bistratified cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord interneuron) AnnotationAssertion(Annotation( "CL:CVS") "A CNS interneuron located in the spinal cord.") -AnnotationAssertion(Annotation( ) "ZFA:0000778") AnnotationAssertion(rdfs:comment "Is_a interneuron, part_of UBERON:0002240.") AnnotationAssertion(rdfs:label "spinal cord interneuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatomotor neuron) AnnotationAssertion(Annotation( "ZFIN:CVS") "A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic.") -AnnotationAssertion(Annotation( ) "ZFA:0005733") AnnotationAssertion( "somatic motor neuron") AnnotationAssertion(rdfs:label "somatomotor neuron"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletogenic cell) @@ -18498,9 +19007,7 @@ SubClassOf( "UBERONREF:0000002") "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.") AnnotationAssertion( ) AnnotationAssertion( "2012-06-27T08:27:35Z") -AnnotationAssertion(Annotation( ) "ZFA:0007084") AnnotationAssertion(rdfs:label "premigratory neural crest cell") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -18533,34 +19040,26 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeletal muscle fiber"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (visceral muscle cell) AnnotationAssertion(Annotation( "GOC:dos") "A muscle cell that is part of some visceral muscle.") -AnnotationAssertion(Annotation( ) "FBbt:00005070") +AnnotationAssertion( "FBbt:00005070") AnnotationAssertion(rdfs:label "visceral muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (striated visceral muscle cell) AnnotationAssertion(Annotation( "GOC:dos") "A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods.") AnnotationAssertion(rdfs:label "striated visceral muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) -SubClassOf( ) # Class: (transversely striated visceral muscle cell) AnnotationAssertion(Annotation( "GOC:dos") "A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods.") AnnotationAssertion(rdfs:label "transversely striated visceral muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (adult skeletal muscle myoblast) @@ -18569,8 +19068,6 @@ AnnotationAssertion(Annotation( "The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins.") AnnotationAssertion(rdfs:label "adult skeletal muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (mesenchymal cell) @@ -18580,7 +19077,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchymal cell") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -18589,29 +19086,19 @@ SubClassOf( ObjectSomeValuesFrom( "PMID:18816864") "A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves.") AnnotationAssertion(rdfs:label "endocardial cushion cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (noradrenergic neuron) AnnotationAssertion(Annotation( "GOC:dos") "A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter.") -AnnotationAssertion(Annotation( ) "ZFA:0005873") AnnotationAssertion(rdfs:label "noradrenergic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (visual system neuron) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any neuron that is capable of part of some visual perception.") AnnotationAssertion( ) AnnotationAssertion( "2017-07-09T19:12:36Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "visual system neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cortical interneuron) @@ -18620,8 +19107,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cortical interneuron"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (mural cell) @@ -18629,7 +19114,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( "2020-02-29T17:33:55Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( ) "ZFA:0005944") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -18638,14 +19122,11 @@ SubClassOf( (microcirculation associated smooth muscle cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any vascular associated smooth muscle cell that is part of some microcirculatory vessel.") AnnotationAssertion( ) AnnotationAssertion( "2020-02-29T17:37:00Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "microcirculation associated smooth muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (sensory neuron of spinal nerve) @@ -18653,8 +19134,7 @@ AnnotationAssertion(Annotation( "spinal sensory neuron") AnnotationAssertion(rdfs:label "sensory neuron of spinal nerve") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "true") ) # Class: (compound eye retinal cell) @@ -18663,8 +19143,6 @@ AnnotationAssertion( "PMID:12021768") AnnotationAssertion(rdfs:label "compound eye retinal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (retinal cell) @@ -18674,7 +19152,6 @@ AnnotationAssertion( "retinal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic skeletal muscle fiber) @@ -18683,8 +19160,6 @@ AnnotationAssertion( "2022-02-21T15:39:10Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "embryonic skeletal muscle fiber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (stromal cell of bone marrow) @@ -18693,8 +19168,6 @@ AnnotationAssertion( "bone marrow stromal cell") AnnotationAssertion(rdfs:label "stromal cell of bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (mononuclear cell of bone marrow) @@ -18703,47 +19176,30 @@ AnnotationAssertion( "bone marrow mononuclear cell") AnnotationAssertion(rdfs:label "mononuclear cell of bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (cardiac blood vessel endothelial cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any blood vessel endothelial cell that is part of some heart.") AnnotationAssertion(rdfs:label "cardiac blood vessel endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (His-Purkinje system cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any cell that is part of some His-Purkinje system.") AnnotationAssertion(rdfs:label "His-Purkinje system cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac endothelial cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any endothelial cell that is part of some heart.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiac endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (camera-type eye photoreceptor cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any photoreceptor cell that is part of some camera-type eye.") AnnotationAssertion( "camera type eye photoreceptor cell") AnnotationAssertion(rdfs:label "camera-type eye photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf(Annotation(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/2245") ObjectSomeValuesFrom( )) # Class: (cerebral cortex neuron) @@ -18759,8 +19215,6 @@ AnnotationAssertion( "cerebral cortex neuron") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/1359") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (zygote) @@ -18772,21 +19226,14 @@ SubClassOf( (cardiac glial cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any glial cell that is part of some heart.") AnnotationAssertion(rdfs:label "cardiac glial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac myoblast) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any myoblast that develops into some cardiac muscle cell.") AnnotationAssertion( "MESH:D032386") AnnotationAssertion(rdfs:label "cardiac myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac neuron) @@ -18796,8 +19243,6 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "cardiac neuron") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/pull/1488") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord motor neuron) @@ -18805,8 +19250,6 @@ AnnotationAssertion(Annotation( "spinal cord motor neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (paraxial cell) @@ -18817,7 +19260,6 @@ AnnotationAssertion( "paraxial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (neural crest cell) @@ -18835,8 +19277,6 @@ AnnotationAssertion( "mesothelial cell of epicardium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of upper back skin) @@ -18845,7 +19285,6 @@ AnnotationAssertion( "fibroblast of upper back skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of skin of back) @@ -18853,8 +19292,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fibroblast of skin of back") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (progenitor cell) @@ -18863,9 +19301,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "progenitor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (skeletal muscle fibroblast) @@ -18875,8 +19311,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "skeletal muscle fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (dermal microvascular endothelial cell) @@ -18886,8 +19321,6 @@ AnnotationAssertion( "dermal microvascular endothelium cell") AnnotationAssertion(rdfs:label "dermal microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (precursor cell) @@ -18896,8 +19329,6 @@ AnnotationAssertion( "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.") AnnotationAssertion(rdfs:label "precursor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuron of the forebrain) @@ -18909,8 +19340,6 @@ AnnotationAssertion( "neuron of the forebrain") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (neutrophillic cytoplasm) @@ -18919,8 +19348,6 @@ AnnotationAssertion( "2010-05-25T01:36:34Z") AnnotationAssertion(rdfs:label "neutrophillic cytoplasm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (acidophilic cytoplasm) @@ -18930,8 +19357,6 @@ AnnotationAssertion( AnnotationAssertion( "eosinophilic") AnnotationAssertion(rdfs:label "acidophilic cytoplasm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (basophilic cytoplasm) @@ -18941,7 +19366,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "basophilic cytoplasm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (polychromatophilic cytoplasm) @@ -18950,8 +19374,6 @@ AnnotationAssertion( "2009-12-28T04:25:23Z") AnnotationAssertion(rdfs:label "polychromatophilic cytoplasm") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (reniform nucleus) @@ -18961,15 +19383,12 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "reniform nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (alobate nucleus) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any nucleus that has characteristic some alobate.") AnnotationAssertion(rdfs:label "alobate nucleus"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (blood vessel smooth muscle cell) @@ -18981,26 +19400,16 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood vessel smooth muscle cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (forebrain neuroblast) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any neuroblast (sensu Vertebrata) that is part of some forebrain.") AnnotationAssertion(rdfs:label "forebrain neuroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (stomach neuroendocrine cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any neuroendocrine cell that is part of some stomach.") AnnotationAssertion(rdfs:label "stomach neuroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) # Class: (lung neuroendocrine cell) @@ -19012,35 +19421,25 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung neuroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung ciliated cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any ciliated cell that is part of some lung.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung ciliated cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung secretory cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any secretory cell that is part of some lung.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung secretory cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (trophectodermal cell) @@ -19055,9 +19454,6 @@ AnnotationAssertion( "FMA:256516") "squamous mesothelial cell of dura mater") AnnotationAssertion(rdfs:label "mesothelial cell of dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of areolar connective tissue) @@ -19075,8 +19471,6 @@ AnnotationAssertion( "fibroblast of tunica adventitia of artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of dense regular elastic tissue) @@ -19086,7 +19480,6 @@ AnnotationAssertion(rdfs:label "fibr EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (epicardial adipocyte) @@ -19099,7 +19492,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epicardial adipocyte") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (adipocyte of epicardial fat of right ventricle) @@ -19110,7 +19502,7 @@ AnnotationAssertion(Annotation( "FMA:261297") "epicardial fat cell of right ventricle") AnnotationAssertion(rdfs:label "adipocyte of epicardial fat of right ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (adipocyte of epicardial fat of left ventricle) @@ -19122,7 +19514,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "adipocyte of epicardial fat of left ventricle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (transitional myocyte of interatrial septum) @@ -19132,8 +19524,6 @@ AnnotationAssertion( "transitional myocyte of interatrial septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (transitional myocyte of interventricular septum) @@ -19142,8 +19532,6 @@ AnnotationAssertion( "transitional myocyte of interventricular septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (Purkinje myocyte of interventricular septum) @@ -19152,8 +19540,6 @@ AnnotationAssertion( "Purkinje myocyte of interventricular septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (myocyte of sinoatrial node) @@ -19167,8 +19553,6 @@ AnnotationAssertion(Annotation( "myocyte of sinoatrial node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (myocyte of atrioventricular node) @@ -19182,9 +19566,6 @@ AnnotationAssertion(Annotation( "myocyte of atrioventricular node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell of arteriole) @@ -19196,7 +19577,6 @@ AnnotationAssertion( "endothelial cell of arteriole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (endothelial cell of artery) @@ -19223,19 +19603,16 @@ AnnotationAssertion( "endothelial cell of venule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (stem cell of epidermis) AnnotationAssertion(Annotation( "GOC:tfm") "A somatic stem cell that is part of the epidermis.") AnnotationAssertion( "FMA:70541") -AnnotationAssertion(Annotation( ) "ZFA:0007122") AnnotationAssertion(Annotation( "FMA:70541") "epidermal stem cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stem cell of epidermis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (ciliary muscle cell) @@ -19247,7 +19624,6 @@ AnnotationAssertion( "ciliary muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of anterior chamber of eye) @@ -19255,8 +19631,6 @@ AnnotationAssertion(Annotation( "FMA:70615") AnnotationAssertion(rdfs:label "mesothelial cell of anterior chamber of eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of parietal peritoneum) @@ -19264,8 +19638,6 @@ AnnotationAssertion(Annotation( "FMA:72142") AnnotationAssertion(rdfs:label "mesothelial cell of parietal peritoneum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of visceral peritoneum) @@ -19275,8 +19647,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell of visceral peritoneum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (transitional myocyte of sinoatrial node) @@ -19286,7 +19656,6 @@ AnnotationAssertion( "transitional myocyte of sinoatrial node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (Purkinje myocyte of atrioventricular node) @@ -19295,7 +19664,6 @@ AnnotationAssertion( "Purkinje myocyte of atrioventricular node") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (myocardial endocrine cell of interventricular septum) @@ -19304,8 +19672,6 @@ AnnotationAssertion( "myocardial endocrine cell of interventricular septum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of peritoneum) @@ -19314,8 +19680,6 @@ AnnotationAssertion( "FMA:86736") "peritoneal mesothelial cell") AnnotationAssertion(rdfs:label "mesothelial cell of peritoneum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of pleura) @@ -19325,8 +19689,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "mesothelial cell of pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of parietal pleura) @@ -19334,8 +19696,6 @@ AnnotationAssertion(Annotation( "FMA:86738") AnnotationAssertion(rdfs:label "mesothelial cell of parietal pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesothelial cell of visceral pleura) @@ -19346,24 +19706,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell of visceral pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung endothelial cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any endothelial cell of vascular tree that is part of some lung.") AnnotationAssertion( "endothelial cell of lung") AnnotationAssertion( "pulmonary vessel endothelial cell") AnnotationAssertion(rdfs:label "lung endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary artery endothelial cell) -AnnotationAssertion(Annotation( "FBC:Autogenerated") "Any endothelial cell of vascular tree that is part of some pulmonary artery.") AnnotationAssertion( ) AnnotationAssertion( "BTO:0001141") AnnotationAssertion(Annotation( "BTO:0001141") "PAEC cell") @@ -19371,7 +19724,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary artery endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (oral mucosa squamous cell) @@ -19384,9 +19736,6 @@ AnnotationAssertion(Annotation( "CALOHA:TS-1252") "oral mucosa squamous epithelial cells") AnnotationAssertion(rdfs:label "oral mucosa squamous cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral cortex glial cell) @@ -19397,8 +19746,6 @@ AnnotationAssertion(Annotation( "CALOHA:TS-1256") "cerebrum cortex glial cell") AnnotationAssertion(rdfs:label "cerebral cortex glial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral cortex endothelial cell) @@ -19409,9 +19756,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "cerebral cortex endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle fibroblast) @@ -19420,8 +19764,6 @@ AnnotationAssertion(Annotation( "CALOHA:TS-0643") AnnotationAssertion(rdfs:label "muscle fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (bone marrow hematopoietic cell) @@ -19431,8 +19773,6 @@ AnnotationAssertion(Annotation( "CALOHA:TS-2109") "bone marrow poietic cells") AnnotationAssertion(rdfs:label "bone marrow hematopoietic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (peripheral blood mononuclear cell) @@ -19444,9 +19784,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peripheral blood mononuclear cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain macroglial cell) @@ -19456,8 +19793,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000005") AnnotationAssertion(rdfs:label "brain macroglial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (microvascular endothelial cell) @@ -19467,8 +19802,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000008") AnnotationAssertion(rdfs:label "microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (dermis blood vessel endothelial cell) @@ -19478,8 +19811,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000010") AnnotationAssertion(rdfs:label "dermis blood vessel endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fibroblast of skin of abdomen) @@ -19489,8 +19820,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000013") AnnotationAssertion(rdfs:label "fibroblast of skin of abdomen") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung microvascular endothelial cell) @@ -19501,7 +19830,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) # Class: (compound eye photoreceptor cell) @@ -19509,12 +19837,10 @@ SubClassOf( "GOC:TermGenie") "Any photoreceptor cell that is part of a compound eye.") AnnotationAssertion( ) AnnotationAssertion( "2014-06-24T23:16:45Z") -AnnotationAssertion(Annotation( ) "FBbt:00006009") +AnnotationAssertion( "FBbt:00004211") AnnotationAssertion( "CL:2000019") AnnotationAssertion(rdfs:label "compound eye photoreceptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (inner cell mass cell) @@ -19524,8 +19850,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000020") AnnotationAssertion(rdfs:label "inner cell mass cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac septum cell) @@ -19535,8 +19859,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000022") AnnotationAssertion(rdfs:label "cardiac septum cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (spinal cord oligodendrocyte) @@ -19546,8 +19868,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000025") AnnotationAssertion(rdfs:label "spinal cord oligodendrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (central nervous system neuron) @@ -19557,13 +19877,10 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000029") AnnotationAssertion(rdfs:label "central nervous system neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (peripheral nervous system neuron) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "ISBN:0721662544") "A neuron that is part of a peripheral nervous system.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2014-06-25T02:28:17Z") AnnotationAssertion( "FMA:84664") @@ -19571,11 +19888,8 @@ AnnotationAssertion( "peripheral neuron") AnnotationAssertion( "CL:2000032") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peripheral nervous system neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic fibroblast) @@ -19586,8 +19900,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryonic fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain microvascular endothelial cell) @@ -19597,9 +19909,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000044") AnnotationAssertion(rdfs:label "brain microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (ventricular cardiac muscle cell) @@ -19610,8 +19919,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ventricular cardiac muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (brainstem motor neuron) @@ -19621,9 +19928,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000047") AnnotationAssertion(rdfs:label "brainstem motor neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian fibroblast) @@ -19634,8 +19938,6 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=7330") AnnotationAssertion(rdfs:label "ovarian fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (ovarian surface epithelial cell) @@ -19647,8 +19949,6 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=7310") AnnotationAssertion(rdfs:label "ovarian surface epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac ventricle fibroblast) @@ -19661,8 +19961,6 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=6310") AnnotationAssertion(rdfs:label "cardiac ventricle fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cardiac atrium fibroblast) @@ -19675,8 +19973,6 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=6320") AnnotationAssertion(rdfs:label "cardiac atrium fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (pericardium fibroblast) @@ -19687,8 +19983,6 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=6430") AnnotationAssertion(rdfs:label "pericardium fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (optic choroid fibroblast) @@ -19699,8 +19993,6 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=6620") AnnotationAssertion(rdfs:label "optic choroid fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (adipose microvascular endothelial cell) @@ -19711,9 +20003,6 @@ AnnotationAssertion( "http://www.sciencellonline.com/site/productInformation.php?keyword=7200") AnnotationAssertion(rdfs:label "adipose microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (migratory cardiac neural crest cell) @@ -19724,8 +20013,6 @@ AnnotationAssertion(Annotation( "CL:2000073") AnnotationAssertion(rdfs:label "migratory cardiac neural crest cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchymal stem cell of abdominal adipose tissue) @@ -19736,8 +20023,6 @@ AnnotationAssertion( "CL:2000080") AnnotationAssertion(rdfs:label "mesenchymal stem cell of abdominal adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (ciliated epithelial cell of esophagus) @@ -19747,9 +20032,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:3000000") AnnotationAssertion(rdfs:label "ciliated epithelial cell of esophagus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (peripheral sensory neuron) @@ -19759,8 +20041,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:3000004") AnnotationAssertion(rdfs:label "peripheral sensory neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (horizontal pyramidal neuron) @@ -19769,9 +20049,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "horizontal pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (brain vascular cell) @@ -19781,8 +20058,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain vascular cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (bitufted neuron) @@ -19792,8 +20067,6 @@ AnnotationAssertion(Annotation( "Int AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bitufted neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (midbrain-derived inhibitory neuron) @@ -19803,9 +20076,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "midbrain-derived inhibitory neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (inverted pyramidal neuron) @@ -19814,9 +20084,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "inverted pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (stellate pyramidal neuron) @@ -19825,9 +20092,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stellate pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (tufted pyramidal neuron) @@ -19836,9 +20100,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tufted pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (untufted pyramidal neuron) @@ -19847,9 +20108,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "untufted pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (cerebral cortex pyramidal neuron) @@ -19857,8 +20115,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "cerebral cortex pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (myelinating glial cell) @@ -19866,8 +20122,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "myelinating glial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (double bouquet cell) @@ -19875,8 +20129,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "double bouquet cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (somatosensory neuron) @@ -19884,8 +20136,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "somatosensory neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary capillary endothelial cell) @@ -19895,7 +20145,6 @@ AnnotationAssertion( AnnotationAssertion( "lung capillary endothelial cell") AnnotationAssertion(rdfs:label "pulmonary capillary endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -19906,8 +20155,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood lymphocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (respiratory ciliated cell) @@ -19916,8 +20163,7 @@ AnnotationAssertion( "ciliated cell of the respiratory tract") AnnotationAssertion(rdfs:label "respiratory ciliated cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (vein endothelial cell of respiratory system) @@ -19927,8 +20173,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vein endothelial cell of respiratory system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (lung megakaryocyte) @@ -19945,8 +20189,6 @@ AnnotationAssertion( "lung megakaryocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (taste receptor cell of tongue) @@ -19956,10 +20198,6 @@ AnnotationAssertion( "DOI:10.1016/s0022-5320(69)80043-2") "gustatory cell of tongue") AnnotationAssertion(rdfs:label "taste receptor cell of tongue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (catecholaminergic neuron) @@ -19969,9 +20207,6 @@ AnnotationAssertion( "PMID:10191060") Annotation( "PMID:12128258") Annotation( "PMID:34880760") Annotation( "https://orcid.org/0000-0002-2244-7917") rdfs:comment "Frequently used when describing the developing nervous system in zebrafish. A catecholaminergic neuron expresses tyrosine hydroxylase (TH), tyrosine hydroxylase 2 (TH2), aromatic amino acid decarboxylase (AADC), dopamine b-hydroxylase (DBH), and phenylethanolamine-N-methyl transferase (PEMT), which are enzymes necessary for catecholamine synthesis.") AnnotationAssertion(rdfs:label "catecholaminergic neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (perivascular cell) @@ -19980,8 +20215,6 @@ AnnotationAssertion( "2023-08-22T13:40:28Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "perivascular cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mesenchymal stem cell of orbital adipose tissue) @@ -19993,8 +20226,23 @@ AnnotationAssertion(Annotation( "PMID:31377878") "orbital adipose-derived mesenchymal stem cell") AnnotationAssertion(rdfs:label "mesenchymal stem cell of orbital adipose tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (reproduction) + +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:isa_complete") Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.") +AnnotationAssertion( "GO:0019952") +AnnotationAssertion( "GO:0050876") +AnnotationAssertion( "Wikipedia:Reproduction") +AnnotationAssertion( "reproductive physiological process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0000003") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "reproduction") +SubClassOf( ) # Class: (vacuole inheritance) @@ -20206,7 +20454,7 @@ AnnotationAssertion( "response to acid anion") AnnotationAssertion( "response to oxoanion") AnnotationAssertion( "GO:0001101") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. 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. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead.") AnnotationAssertion(rdfs:label "response to acid chemical") SubClassOf( ) @@ -20268,7 +20516,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "ciliary or bacterial-type flagellar motility") AnnotationAssertion( "GO:0001539") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent, while the bacterial- and archaeal-type flagella have a different structure. The former are microtubule-based structures that lash back and forth and are present only in eukaryotes, while the latter achieve motility by rotation. Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. These three structures never co-exist in the same organism. Therefore, GO:0001539 'cilium or flagellum-dependent cell motility' is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term. Direct annotations to GO:0001539 'cilium or flagellum-dependent cell motility' may be amended during annotation QC.") AnnotationAssertion(rdfs:label "cilium or flagellum-dependent cell motility") SubClassOf( ) @@ -20310,23 +20558,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (regulation of cell growth by extracellular stimulus) - -AnnotationAssertion(Annotation( "GOC:dph") "Any process in which external signals modulate the frequency, rate or extent of cell growth, the irreversible increase in size of a cell over time.") -AnnotationAssertion( "interpretation of external signals that regulate cell growth") -AnnotationAssertion( "regulation of cell growth by detection of exogenous stimulus") -AnnotationAssertion( "regulation of cell growth by sensing of exogenous stimulus") -AnnotationAssertion( "regulation of growth by exogenous signal") -AnnotationAssertion( "regulation of growth by exogenous stimuli") -AnnotationAssertion( "regulation of growth by exogenous stimulus") -AnnotationAssertion( "regulation of growth by external signal") -AnnotationAssertion( "regulation of growth by external stimuli") -AnnotationAssertion( "regulation of growth by external stimulus") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0001560") -AnnotationAssertion(rdfs:label "regulation of cell growth by extracellular stimulus") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (blood vessel development) AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "UBERON:0001981") "The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.") @@ -21725,7 +21956,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0002790") AnnotationAssertion(rdfs:label "peptide secretion") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -21773,7 +22004,7 @@ SubClassOf( "GOC:add") "Any process that modulates the frequency, rate, or extent of a response to biotic stimulus.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002831") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of response to biotic stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -21787,7 +22018,7 @@ AnnotationAssertion( "inhibition of response to biotic stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002832") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of response to biotic stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -21802,7 +22033,7 @@ AnnotationAssertion( "stimulation of response to biotic stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002833") -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 "positive regulation of response to biotic stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -21869,7 +22100,7 @@ AnnotationAssertion( "GOC:dph") Annotation( "GOC:tb") "reproductive developmental process") AnnotationAssertion( "GO:0003006") AnnotationAssertion(rdfs:label "developmental process involved in reproduction") -EquivalentClasses( ObjectIntersectionOf( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -22825,7 +23056,7 @@ AnnotationAssertion( "GO:0003333") AnnotationAssertion(rdfs:comment "Note that this term is not intended for use in annotating lateral movement within membranes.") AnnotationAssertion(rdfs:label "amino acid transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (cilium movement) @@ -23172,6 +23403,42 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (molecular_function) + +AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") +AnnotationAssertion( "GO:0005554") +AnnotationAssertion( "molecular function") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0003674") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (catalytic activity) + +AnnotationAssertion(Annotation( "GOC:vw") Annotation( "ISBN:0198506732") "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.") +AnnotationAssertion( "Wikipedia:Enzyme") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "enzyme activity") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0003824") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "catalytic activity") +SubClassOf( ) + # Class: (cellular_component) AnnotationAssertion(Annotation( "GOC:pdt") "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).") @@ -23204,16 +23471,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.") AnnotationAssertion(rdfs:label "extracellular region") @@ -23294,6 +23558,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term.") AnnotationAssertion(rdfs:label "extracellular space") SubClassOf( ) @@ -23332,14 +23597,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleus") SubClassOf( ) @@ -23397,7 +23660,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.") AnnotationAssertion(rdfs:label "chromosome") @@ -23435,9 +23697,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cytoplasm") SubClassOf( ) @@ -23454,13 +23714,11 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vacuole") SubClassOf( ) @@ -23499,12 +23757,10 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.") AnnotationAssertion(rdfs:label "Golgi apparatus") @@ -23536,7 +23792,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -23560,14 +23815,11 @@ AnnotationAssertion( "GO:0005840") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ribosome") SubClassOf( ) @@ -23585,13 +23837,11 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cytoskeleton") @@ -23681,14 +23931,11 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "plasma membrane") SubClassOf( ) @@ -23812,7 +24059,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -23915,6 +24161,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleobase-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) # Class: (DNA metabolic process) @@ -23932,10 +24179,9 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "DNA metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (chromatin organization) @@ -24020,14 +24266,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "translation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -24130,7 +24374,7 @@ AnnotationAssertion( "GO:0006518") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peptide metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (amino acid metabolic process) @@ -24149,7 +24393,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -24237,16 +24480,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lipid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -24271,6 +24511,19 @@ SubClassOf( ) SubClassOf( ) +# Class: (cellular aromatic compound metabolic process) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.") +AnnotationAssertion( "aromatic compound metabolism") +AnnotationAssertion( "aromatic hydrocarbon metabolic process") +AnnotationAssertion( "aromatic hydrocarbon metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006725") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cellular aromatic compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (sulfur compound metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.") @@ -24290,6 +24543,40 @@ AnnotationAssertion(rdfs:label "sulf EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (phosphorus metabolic process) + +AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).") +AnnotationAssertion( "phosphorus metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006793") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphorus metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (phosphate-containing compound metabolic process) + +AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.") +AnnotationAssertion( "phosphate metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "phosphate metabolic process") +AnnotationAssertion( "GO:0006796") +AnnotationAssertion(rdfs:label "phosphate-containing compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (nitrogen compound metabolic process) + +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) +AnnotationAssertion( "nitrogen compound metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006807") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nitrogen compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (transport) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:mah") "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.") @@ -24308,9 +24595,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that 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, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.") AnnotationAssertion(rdfs:label "transport") SubClassOf( ) @@ -24327,6 +24612,29 @@ AnnotationAssertion( "monoatomic ion transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (monoatomic cation transport) + +AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom.") +AnnotationAssertion( "GO:0006819") +AnnotationAssertion( "GO:0015674") +AnnotationAssertion( "GO:0072512") +AnnotationAssertion( "cation transport") +AnnotationAssertion(Annotation( "GOC:mah") "di-, tri-valent inorganic cation transport") +AnnotationAssertion( "trivalent inorganic cation transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006812") +AnnotationAssertion(rdfs:label "monoatomic cation transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (phosphate ion transport) + +AnnotationAssertion(Annotation( "GOC:krc") "The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "phosphate transport") +AnnotationAssertion( "GO:0006817") +AnnotationAssertion(rdfs:label "phosphate ion transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (neurotransmitter transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.") @@ -24389,7 +24697,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino acid transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (lipid transport) @@ -24403,6 +24711,28 @@ AnnotationAssertion(rdfs:label "lipi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (intracellular monoatomic ion homeostasis) + +AnnotationAssertion(Annotation( "GOC:mah") "A homeostatic process involved in the maintenance of a steady state level of monoatomic ions within a cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) +AnnotationAssertion( "cellular ion homeostasis") +AnnotationAssertion( "cellular monoatomic ion homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006873") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "intracellular monoatomic ion homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (regulation of pH) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:go_curators") Annotation( "GOC:tb") "Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "hydrogen ion homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006885") +AnnotationAssertion(rdfs:label "regulation of pH") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (intracellular protein transport) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.") @@ -24628,12 +24958,12 @@ AnnotationAssertion( "response to abiotic stress") AnnotationAssertion( "response to biotic stress") AnnotationAssertion( "GO:0006950") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) 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( ) @@ -24668,7 +24998,6 @@ SubClassOf( ObjectAllValuesFrom( (organelle 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 an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-19T15:25:51Z") AnnotationAssertion( "GO:1902589") @@ -24678,10 +25007,8 @@ AnnotationAssertion( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:mah") "organelle organization and biogenesis") AnnotationAssertion( "single-organism organelle organization") AnnotationAssertion( "GO:0006996") -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 "organelle organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -24906,14 +25233,13 @@ AnnotationAssertion( "cell-division cycle") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0007049") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell cycle") SubClassOf( ) @@ -25053,17 +25379,20 @@ AnnotationAssertion( "GO:0023033") AnnotationAssertion( "GO:0023045") AnnotationAssertion( "Wikipedia:Signal_transduction") +AnnotationAssertion( "signal transduction by cis-phosphorylation") +AnnotationAssertion( "signal transduction by conformational transition") +AnnotationAssertion( "signal transduction by protein phosphorylation") +AnnotationAssertion( "signal transduction by trans-phosphorylation") AnnotationAssertion( "signaling cascade") AnnotationAssertion( "signalling cascade") AnnotationAssertion( "biological_process") AnnotationAssertion( "signaling pathway") -AnnotationAssertion( "signalling pathway") +AnnotationAssertion(Annotation( "GOC:mah") "signalling pathway") AnnotationAssertion( "GO:0007165") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.") AnnotationAssertion(rdfs:label "signal transduction") SubClassOf( ) @@ -25482,7 +25811,6 @@ SubClassOf( ObjectSomeValuesFrom( (heart development) AnnotationAssertion(Annotation( "GOC:jid") Annotation( "UBERON:0000948") "The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.") -AnnotationAssertion( ) AnnotationAssertion( "GO:0007511") AnnotationAssertion( "Wikipedia:Heart_development") AnnotationAssertion( "dorsal vessel development") @@ -25641,7 +25969,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism behavior") AnnotationAssertion( "GO:0007610") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "1. 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 reviews. @@ -25790,7 +26118,6 @@ SubClassOf( (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( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-17T15:46:40Z") AnnotationAssertion( "GO:0044236") @@ -25803,13 +26130,11 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism metabolic process") AnnotationAssertion( "GO:0008152") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -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( ) @@ -25948,7 +26273,6 @@ SubClassOf( ObjectAllValuesFrom( "GOC:bf") Annotation( "GOC:jl") "The orderly movement of a cell specialized to produce haploid gametes through the embryo from its site of production to the place where the gonads will form.") AnnotationAssertion( "germ-cell migration") -AnnotationAssertion( "pole cell migration") AnnotationAssertion( "biological_process") AnnotationAssertion( "primordial germ cell migration") AnnotationAssertion( "GO:0008354") @@ -26070,7 +26394,6 @@ SubClassOf( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17904"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27304"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Amino_acid_synthesis") AnnotationAssertion( "amino acid anabolism") AnnotationAssertion( "amino acid biosynthesis") @@ -26080,7 +26403,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0008652") AnnotationAssertion(rdfs:label "amino acid biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (biosynthetic process) @@ -26101,7 +26424,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "biosynthetic process") SubClassOf( ) @@ -26110,7 +26432,6 @@ SubClassOf( "GOC:mah") "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15249"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25418"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "GO:0043284") AnnotationAssertion(Annotation( "GOC:mtg_chebi_dec09") "biopolymer biosynthetic process") AnnotationAssertion( "macromolecule anabolism") @@ -26119,9 +26440,7 @@ AnnotationAssertion( "macromolecule synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009059") -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 "macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -26202,7 +26521,7 @@ AnnotationAssertion( "GO:0009309") AnnotationAssertion(rdfs:label "amine biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) # Class: (response to radiation) @@ -26298,7 +26617,7 @@ AnnotationAssertion(Annotation( "response to environmental stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009605") -AnnotationAssertion( ) +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.") @@ -26311,7 +26630,7 @@ AnnotationAssertion(Annotation( "response to biotic stress") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009607") -AnnotationAssertion( ) +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.") @@ -26348,7 +26667,7 @@ AnnotationAssertion( "response to abiotic stress") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009628") -AnnotationAssertion( ) +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.") @@ -26411,7 +26730,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:sm") "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 arising within the organism.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009719") -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 endogenous stimulus") @@ -26420,8 +26739,6 @@ SubClassOf( (response to hormone) AnnotationAssertion(Annotation( "GOC:jl") "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 hormone stimulus.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(Annotation( "GOC:dos") "response to hormone stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "growth regulator") @@ -26429,12 +26746,6 @@ AnnotationAssertion( "response to hormone") SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) -SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) -DisjointClasses( ObjectSomeValuesFrom( )) -DisjointClasses( ObjectSomeValuesFrom( )) # Class: (response to carbohydrate) @@ -26463,7 +26774,7 @@ AnnotationAssertion( "embryonal development") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009790") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryo development") @@ -26540,8 +26851,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) # Class: (tissue development) @@ -26820,13 +27129,10 @@ SubClassOf( (response to organic substance) AnnotationAssertion(Annotation( "GOC:sm") Annotation( "PMID:23356676") "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 organic substance stimulus.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "GO:1990367") AnnotationAssertion( "process resulting in tolerance to organic substance") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010033") -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 organic substance") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -26882,12 +27188,9 @@ SubClassOf( (response to organonitrogen compound) AnnotationAssertion(Annotation( "PMID:9869419") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "response to organic nitrogen") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010243") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "response to organonitrogen compound") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -26970,8 +27273,6 @@ AnnotationAssertion( "GOC:cjm") "gene regulation") AnnotationAssertion( "regulation of gene product expression") AnnotationAssertion( "GO:0010468") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.") AnnotationAssertion(rdfs:label "regulation of gene expression") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -27083,6 +27384,22 @@ AnnotationAssertion( "negative regulation of glycoprotein biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (positive regulation of phosphorus metabolic process) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0010562") +AnnotationAssertion(rdfs:label "positive regulation of phosphorus metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of phosphorus metabolic process) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0010563") +AnnotationAssertion(rdfs:label "negative regulation of phosphorus metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of cell cycle process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.") @@ -27789,6 +28106,16 @@ AnnotationAssertion( "regulation of amino acid import across plasma membrane") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of phosphate transport) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of phosphate transport. Phosphate transport is the directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2009-05-20T11:42:50Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0010966") +AnnotationAssertion(rdfs:label "regulation of phosphate transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of microtubule nucleation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell.") @@ -27876,11 +28203,9 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "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") @@ -28688,7 +29013,7 @@ AnnotationAssertion( "GO:0015833") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peptide transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -28826,12 +29151,10 @@ AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mah") "cell organization and biogenesis") AnnotationAssertion( "GO:0016043") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -28920,7 +29243,6 @@ AnnotationAssertion( "GO:0016070") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -28942,7 +29264,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -28959,6 +29280,35 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) 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( "molecular_function") +AnnotationAssertion( "GO:0016301") +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( ) +SubClassOf( ObjectHasSelf()) + +# 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( "Wikipedia:Phosphorylation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0016310") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "phosphorylation") +SubClassOf( ) + # Class: (female meiosis chromosome segregation) AnnotationAssertion(Annotation( "GOC:ai") "The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female.") @@ -29048,6 +29398,40 @@ SubClassOf( ObjectComplementOf(Object SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses( ObjectSomeValuesFrom( )) +# Class: (transferase activity) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") +AnnotationAssertion( "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") +AnnotationAssertion(Annotation(rdfs:label "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK") "Reactome:R-HSA-5668414") +AnnotationAssertion(Annotation(rdfs:label "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248") "Reactome:R-HSA-8868783") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0016740") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "transferase activity") +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( "molecular_function") +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: (response to insecticide) AnnotationAssertion(Annotation( "GOC:curators") "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 insecticide stimulus. Insecticides are chemicals used to kill insects.") @@ -29109,6 +29493,20 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (heterocycle biosynthetic process) + +AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).") +AnnotationAssertion( "heterocycle anabolism") +AnnotationAssertion( "heterocycle biosynthesis") +AnnotationAssertion( "heterocycle formation") +AnnotationAssertion( "heterocycle synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0018130") +AnnotationAssertion(rdfs:label "heterocycle biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (phenol-containing compound metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring.") @@ -29123,6 +29521,7 @@ AnnotationAssertion( "Note that phenol metabolism is not included as a child of 'xenobiotic metabolism' because although it is synthesized industrially, phenol is also found naturally in animal wastes and other organic materials. It is often formed by the activity of microorganisms, which can chemically modify a variety of xenobiotic and naturally occurring phenolic compounds.") AnnotationAssertion(rdfs:label "phenol-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -29143,7 +29542,7 @@ AnnotationAssertion( "single-organism reproductive behavior") AnnotationAssertion( "GO:0019098") AnnotationAssertion(rdfs:label "reproductive behavior") -EquivalentClasses( ObjectIntersectionOf( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (regulation of lipid metabolic process) @@ -29175,6 +29574,15 @@ AnnotationAssertion( "regulation of nucleobase-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (regulation of phosphate metabolic process) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.") +AnnotationAssertion( "regulation of phosphate metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0019220") +AnnotationAssertion(rdfs:label "regulation of phosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.") @@ -29235,11 +29643,26 @@ AnnotationAssertion( "acetate biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (aromatic compound biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.") +AnnotationAssertion( "aromatic compound anabolism") +AnnotationAssertion( "aromatic compound biosynthesis") +AnnotationAssertion( "aromatic compound formation") +AnnotationAssertion( "aromatic compound synthesis") +AnnotationAssertion( "aromatic hydrocarbon biosynthesis") +AnnotationAssertion( "aromatic hydrocarbon biosynthetic process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0019438") +AnnotationAssertion(rdfs:label "aromatic compound biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (protein metabolic process) AnnotationAssertion(Annotation( "GOC:ma") "The chemical reactions and pathways involving a protein. Includes protein modification.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "GO:0006411") AnnotationAssertion( "GO:0044267") AnnotationAssertion( "GO:0044268") @@ -29252,14 +29675,11 @@ AnnotationAssertion( "multicellular organismal protein metabolic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019538") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) 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 "protein metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -29270,7 +29690,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0019725") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular homeostasis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -29288,10 +29707,8 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019748") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "secondary metabolic process") SubClassOf( ) @@ -29334,7 +29751,7 @@ AnnotationAssertion( "GO:0019953") AnnotationAssertion(rdfs:comment "Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.") AnnotationAssertion(rdfs:label "sexual reproduction") -SubClassOf( ) +SubClassOf( ) # Class: (prechordal plate formation) @@ -30571,7 +30988,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0022402") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell cycle process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -30587,15 +31003,12 @@ SubClassOf( (cellular component disassembly) AnnotationAssertion(Annotation( "GOC:isa_complete") "A cellular process that results in the breakdown of a cellular component.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "GO:0071845") AnnotationAssertion( "cell structure disassembly") AnnotationAssertion( "cellular component disassembly at cellular level") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022411") -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 "cellular component disassembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -30609,30 +31022,22 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022412") AnnotationAssertion(rdfs:label "cellular process involved in reproduction in multicellular organism") -EquivalentClasses( ObjectIntersectionOf( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (reproductive process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:isa_complete") "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:56:06Z") AnnotationAssertion( "GO:0044702") -AnnotationAssertion( "Wikipedia:Reproduction") AnnotationAssertion( "biological_process") AnnotationAssertion( "single organism reproductive process") AnnotationAssertion( "GO:0022414") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reproductive process") -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (digestive system process) @@ -30674,7 +31079,6 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022607") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -30777,13 +31181,11 @@ AnnotationAssertion(Annotation( "single organism signaling") AnnotationAssertion( "GO:0023052") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.") AnnotationAssertion(rdfs:label "signaling") @@ -30828,6 +31230,17 @@ AnnotationAssertion(rdfs:label "sign EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (intracellular monoatomic cation homeostasis) + +AnnotationAssertion(Annotation( "GOC:ceb") Annotation( "GOC:mah") "A homeostatic process involved in the maintenance of a steady state level of monoatomic cations within a cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) +AnnotationAssertion( "cellular cation homeostasis") +AnnotationAssertion( "cellular monoatomic cation homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0030003") +AnnotationAssertion(rdfs:label "intracellular monoatomic cation homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (establishment of cell polarity) AnnotationAssertion(Annotation( "GOC:mah") "The specification and formation of anisotropic intracellular organization or cell growth patterns.") @@ -30969,8 +31382,6 @@ AnnotationAssertion( "GO:0030097") AnnotationAssertion(rdfs:label "hemopoiesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) # Class: (lymphocyte differentiation) @@ -31041,7 +31452,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell differentiation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -31394,6 +31804,30 @@ AnnotationAssertion( "smooth muscle contractile fiber") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (intracellular sulfate ion homeostasis) + +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:24193406") "A homeostatic process involved in the maintenance of a steady state level of sulfate ions within a cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24514"^^xsd:anyURI) +AnnotationAssertion( "sulphate ion homeostasis") +AnnotationAssertion( "cellular sulfate ion homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0030642") +AnnotationAssertion(rdfs:label "intracellular sulfate ion homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (intracellular phosphate ion homeostasis) + +AnnotationAssertion(Annotation( "GOC:mah") "A homeostatic process involved in the maintenance of a steady state level of phosphate ions within a cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26429"^^xsd:anyURI) +AnnotationAssertion( "intracellular phosphate homeostasis") +AnnotationAssertion( "cellular phosphate ion homeostasis") +AnnotationAssertion( "intracellular Pi homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0030643") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "intracellular phosphate ion homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (transport vesicle membrane) AnnotationAssertion(Annotation( "GOC:mah") "The lipid bilayer surrounding a transport vesicle.") @@ -31632,7 +32066,6 @@ AnnotationAssertion( "GO:0031012") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -31870,12 +32303,10 @@ SubClassOf( ObjectSomeValuesFrom( (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( "biological_process") 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( ) @@ -31884,7 +32315,6 @@ SubClassOf( (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") @@ -31893,7 +32323,6 @@ AnnotationAssertion( "biological_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( ) @@ -31903,7 +32332,6 @@ SubClassOf( (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") @@ -31913,7 +32341,6 @@ AnnotationAssertion( "biological_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( ) @@ -31923,15 +32350,12 @@ SubClassOf( (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( "biological_process") 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( ) @@ -31940,7 +32364,6 @@ SubClassOf( (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") @@ -31951,8 +32374,6 @@ AnnotationAssertion( "inhibition of cellular biosynthetic process") AnnotationAssertion( "biological_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( ) @@ -31962,7 +32383,6 @@ SubClassOf( (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") @@ -31974,8 +32394,6 @@ AnnotationAssertion( "stimulation of cellular biosynthetic process") AnnotationAssertion( "biological_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( ) @@ -32149,6 +32567,15 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of buoyancy) + +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PATO:0001420") "Any process that modulates an organism's tendency or ability to rise or float in a fluid medium such as water or air, often through the use of stored gases.") +AnnotationAssertion( "buoyancy regulation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0031413") +AnnotationAssertion(rdfs:label "regulation of buoyancy") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (protein-containing complex localization) AnnotationAssertion(Annotation( "GOC:mah") "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.") @@ -32232,8 +32659,6 @@ AnnotationAssertion( "positive regulation of myelination") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) # Class: (regulation of nervous system process) @@ -32297,7 +32722,7 @@ AnnotationAssertion( "GO:0031967") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle envelope") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -32321,6 +32746,15 @@ AnnotationAssertion(rdfs:label "memb SubClassOf( ) DisjointClasses( ) +# Class: (envelope) + +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:pz") "A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0031975") +AnnotationAssertion(rdfs:label "envelope") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (nuclear lumen) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:pz") "The volume enclosed by the nuclear inner membrane.") @@ -32407,7 +32841,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of a response to an external stimulus.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032101") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of response to external stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -32422,7 +32856,7 @@ AnnotationAssertion( "inhibition of response to external stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032102") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of response to external stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -32439,7 +32873,7 @@ AnnotationAssertion( "stimulation of response to external stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032103") -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 "positive regulation of response to external stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -32682,6 +33116,17 @@ SubClassOf( ) SubClassOf( ) +# Class: (intracellular oxygen homeostasis) + +AnnotationAssertion(Annotation( "GOC:rph") "A homeostatic process involved in the maintenance of a steady state level of oxygen within a cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24224"^^xsd:anyURI) +AnnotationAssertion( "oxygen homeostasis") +AnnotationAssertion( "cellular oxygen homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032364") +AnnotationAssertion(rdfs:label "intracellular oxygen homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (intracellular lipid transport) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of lipids within cells.") @@ -32800,7 +33245,6 @@ EquivalentClasses( ObjectIntersection # Class: (multicellular organismal process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -32815,7 +33259,6 @@ AnnotationAssertion( "GO:0032501") 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 "multicellular organismal process") SubClassOf( ) SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) @@ -32847,6 +33290,16 @@ AnnotationAssertion( "developmental process") SubClassOf( ) +# Class: (multicellular organism reproduction) + +AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:jid") "The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032504") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "multicellular organism reproduction") +SubClassOf( ) +SubClassOf( ) + # Class: (maintenance of protein location in cell) AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:mah") "Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.") @@ -32982,11 +33435,9 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of localization) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:mah") "regulation of localisation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032879") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of localization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -33224,7 +33675,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032973") AnnotationAssertion(rdfs:label "amino acid export across plasma membrane") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (amino acid transmembrane export from vacuole) @@ -33234,7 +33685,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032974") AnnotationAssertion(rdfs:label "amino acid transmembrane export from vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (amino acid transmembrane import into vacuole) @@ -33243,7 +33694,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0032975") AnnotationAssertion(rdfs:label "amino acid transmembrane import into vacuole") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (protein-containing complex disassembly) @@ -33296,7 +33747,7 @@ AnnotationAssertion( "GO:0032989") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular anatomical entity morphogenesis") -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (protein-containing complex) @@ -33311,7 +33762,6 @@ AnnotationAssertion( "GO:0032991") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -33557,6 +34007,14 @@ AnnotationAssertion( "protein localization to secretory granule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (carbohydrate homeostasis) + +AnnotationAssertion(Annotation( "GOC:mah") "A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0033500") +AnnotationAssertion(rdfs:label "carbohydrate homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (negative regulation of catecholamine secretion) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine.") @@ -33588,6 +34046,36 @@ SubClassOf( ) SubClassOf( ) +# 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( "biological_process") +AnnotationAssertion( "GO:0033673") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negative regulation of kinase activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") 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( "biological_process") +AnnotationAssertion( "GO:0033674") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positive regulation of kinase activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) + # Class: (ribosome localization) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a ribosome is transported to, and/or maintained in, a specific location.") @@ -33867,7 +34355,7 @@ AnnotationAssertion( "GO:0034487") AnnotationAssertion(rdfs:comment "Note that this term is not intended for use in annotating lateral movement within membranes.") AnnotationAssertion(rdfs:label "vacuolar amino acid transmembrane transport") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (protein localization to chromosome) @@ -33893,6 +34381,19 @@ AnnotationAssertion( "protein localization to nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (cellular nitrogen compound metabolic process) + +AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) +AnnotationAssertion( "cellular nitrogen compound metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0034641") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cellular nitrogen compound metabolic process") +SubClassOf( ) +SubClassOf( ) + # Class: (nucleobase-containing compound biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.") @@ -33904,6 +34405,7 @@ AnnotationAssertion( "GO:0034654") AnnotationAssertion(rdfs:label "nucleobase-containing compound biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (regulation of transmembrane transport) @@ -34238,6 +34740,18 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "acetate transmembrane transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +# Class: (phosphate ion transmembrane transport) + +AnnotationAssertion(Annotation( "GOC:vw") "The process in which a phosphate is transported across a membrane.") +AnnotationAssertion( "bf") +AnnotationAssertion( "2010-04-08T11:24:06Z") +AnnotationAssertion( "phosphate ion membrane transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0035435") +AnnotationAssertion(rdfs:comment "Note that this term is not intended for use in annotating lateral movement within membranes.") +AnnotationAssertion(rdfs:label "phosphate ion transmembrane transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (cell migration involved in vasculogenesis) AnnotationAssertion(Annotation( "GOC:dgh") "The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form de novo blood vessels and tubes.") @@ -35058,12 +35572,11 @@ AnnotationAssertion(Annotation( "response to chemical substance") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042221") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) 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 chemical") @@ -35084,7 +35597,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ribosome biogenesis") SubClassOf( ) @@ -35143,6 +35655,39 @@ AnnotationAssertion( "negative regulation of protein import into nucleus") EquivalentClasses( ObjectIntersectionOf( 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( "biological_process") +AnnotationAssertion( "GO:0042325") +AnnotationAssertion(rdfs:label "regulation of phosphorylation") +EquivalentClasses( ObjectIntersectionOf( 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( "down regulation of phosphorylation") +AnnotationAssertion( "down-regulation of phosphorylation") +AnnotationAssertion( "downregulation of phosphorylation") +AnnotationAssertion( "inhibition of phosphorylation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0042326") +AnnotationAssertion(rdfs:label "negative regulation of phosphorylation") +EquivalentClasses( ObjectIntersectionOf( 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( "biological_process") +AnnotationAssertion( "GO:0042327") +AnnotationAssertion(rdfs:label "positive regulation of phosphorylation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of membrane potential) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mtg_cardio") Annotation( "GOC:tb") Annotation( "ISBN:0198506732") "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.") @@ -35249,6 +35794,9 @@ AnnotationAssertion( "GO:0042430") AnnotationAssertion(rdfs:label "indole-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -35265,8 +35813,12 @@ AnnotationAssertion( "GO:0042435") AnnotationAssertion(rdfs:label "indole-containing compound biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (photoreceptor cell development) @@ -35441,7 +35993,6 @@ SubClassOf( (regulation of apoptotic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mtg_apoptosis") "Any process that modulates the occurrence or rate of cell death by apoptotic process.") -AnnotationAssertion( ) AnnotationAssertion( "regulation of apoptosis") AnnotationAssertion( "biological_process") AnnotationAssertion( "apoptosis regulator activity") @@ -35449,9 +36000,6 @@ AnnotationAssertion( "This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.") AnnotationAssertion(rdfs:label "regulation of apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) -DisjointClasses( ObjectSomeValuesFrom( )) # Class: (cell projection) @@ -35462,12 +36010,10 @@ AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0042995") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell projection") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -35587,7 +36133,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043043") AnnotationAssertion(rdfs:label "peptide biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (extracellular structure organization) @@ -35621,7 +36167,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of apoptotic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.") -AnnotationAssertion( ) AnnotationAssertion( "GO:0006916") AnnotationAssertion( "anti-apoptosis") AnnotationAssertion( "down regulation of apoptosis") @@ -35636,9 +36181,6 @@ AnnotationAssertion( "This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.") AnnotationAssertion(rdfs:label "negative regulation of apoptotic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) -DisjointClasses( ObjectSomeValuesFrom( )) # Class: (regulation of programmed cell death) @@ -35689,6 +36231,49 @@ AnnotationAssertion(rdfs:label "germ EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (positive regulation of catalytic activity) + +AnnotationAssertion(Annotation( "GOC:ebc") Annotation( "GOC:jl") Annotation( "GOC:tb") Annotation( "GOC:vw") "Any process that activates or increases the activity of an enzyme.") +AnnotationAssertion( "GO:0048554") +AnnotationAssertion(Annotation( "GOC:tb") "positive regulation of enzyme activity") +AnnotationAssertion( "up regulation of enzyme activity") +AnnotationAssertion( "up-regulation of enzyme activity") +AnnotationAssertion( "upregulation of enzyme activity") +AnnotationAssertion( "activation of enzyme activity") +AnnotationAssertion( "activation of metalloenzyme activity") +AnnotationAssertion( "positive regulation of metalloenzyme activity") +AnnotationAssertion( "stimulation of enzyme activity") +AnnotationAssertion( "stimulation of metalloenzyme activity") +AnnotationAssertion( "up regulation of metalloenzyme activity") +AnnotationAssertion( "up-regulation of metalloenzyme activity") +AnnotationAssertion( "upregulation of metalloenzyme activity") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0043085") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positive regulation of catalytic activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of catalytic activity) + +AnnotationAssertion(Annotation( "GOC:ebc") Annotation( "GOC:jl") Annotation( "GOC:tb") Annotation( "GOC:vw") "Any process that stops or reduces the activity of an enzyme.") +AnnotationAssertion( "GO:0048553") +AnnotationAssertion( "down regulation of enzyme activity") +AnnotationAssertion( "down-regulation of enzyme activity") +AnnotationAssertion( "down-regulation of metalloenzyme activity") +AnnotationAssertion( "downregulation of enzyme activity") +AnnotationAssertion(Annotation( "GOC:tb") "negative regulation of enzyme activity") +AnnotationAssertion( "down regulation of metalloenzyme activity") +AnnotationAssertion( "downregulation of metalloenzyme activity") +AnnotationAssertion( "inhibition of enzyme activity") +AnnotationAssertion( "inhibition of metalloenzyme activity") +AnnotationAssertion( "negative regulation of metalloenzyme activity") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0043086") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negative regulation of catalytic activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of translation by machinery localization) AnnotationAssertion(Annotation( "GOC:jl") "Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location.") @@ -35750,7 +36335,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0043200") AnnotationAssertion(rdfs:label "response to amino acid") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (response to external biotic stimulus) @@ -35791,7 +36376,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle") SubClassOf( ) @@ -35996,20 +36580,17 @@ AnnotationAssertion( "response to alkaloid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (contractile muscle fiber) +# Class: (contractile fiber) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0815316194") "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27281"^^xsd:anyURI) AnnotationAssertion( "contractile fibre") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0043292") -AnnotationAssertion(rdfs:label "contractile muscle fiber") +AnnotationAssertion(rdfs:label "contractile fiber") SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) # Class: (enucleate erythrocyte differentiation) @@ -36232,6 +36813,16 @@ AnnotationAssertion( "endothelial cell migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# 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( "biological_process") +AnnotationAssertion( "GO:0043549") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulation of kinase activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) + # 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.") @@ -36295,14 +36886,11 @@ SubClassOf( ObjectSomeValuesFrom( (amide metabolic process) AnnotationAssertion(Annotation( "GOC:curators") "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "amide metabolism") AnnotationAssertion( "cellular amide metabolic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043603") -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 "amide metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -36314,6 +36902,7 @@ AnnotationAssertion( "amide biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) # Class: (ossification involved in bone maturation) @@ -36442,6 +37031,30 @@ AnnotationAssertion( "membrane biogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (negative regulation of molecular function) + +AnnotationAssertion(Annotation( "GO:jl") "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2009-04-21T04:07:27Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0044092") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negative regulation of molecular function") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (positive regulation of molecular function) + +AnnotationAssertion(Annotation( "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( "jl") +AnnotationAssertion( "2009-04-21T04:11:06Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0044093") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positive regulation of molecular function") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (translation initiation ternary complex) AnnotationAssertion(Annotation( "GOC:jl") "A ribonucleoprotein complex that contains 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).") @@ -36476,29 +37089,36 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044238") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "primary metabolic process") 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( "biological_process") 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 nitrogen compound biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.") +AnnotationAssertion( "nitrogen compound anabolism") +AnnotationAssertion( "nitrogen compound biosynthesis") +AnnotationAssertion( "nitrogen compound formation") +AnnotationAssertion( "nitrogen compound synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0044271") +AnnotationAssertion(rdfs:label "cellular nitrogen compound biosynthetic 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.") @@ -36538,7 +37158,6 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044283") AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.") AnnotationAssertion(rdfs:label "small molecule biosynthetic process") SubClassOf( ) @@ -36827,7 +37446,6 @@ AnnotationAssertion(Annotation( "GO:0045202") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -37792,6 +38410,25 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (pH reduction) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that reduces the internal pH of an organism, part of an organism or a cell, measured by the concentration of the hydrogen ion.") +AnnotationAssertion( "acidification") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045851") +AnnotationAssertion(rdfs:label "pH reduction") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (pH elevation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that increases the internal pH of an organism, part of an organism or a cell, measured by the concentration of the hydrogen ion.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045852") +AnnotationAssertion(rdfs:label "pH elevation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (negative regulation of translational elongation) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.") @@ -38053,6 +38690,33 @@ AnnotationAssertion( "positive regulation of nucleobase-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (negative regulation of phosphate 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 phosphates.") +AnnotationAssertion( "down regulation of phosphate metabolic process") +AnnotationAssertion( "down-regulation of phosphate metabolic process") +AnnotationAssertion( "downregulation of phosphate metabolic process") +AnnotationAssertion( "negative regulation of phosphate metabolism") +AnnotationAssertion( "inhibition of phosphate metabolic process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045936") +AnnotationAssertion(rdfs:label "negative regulation of phosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of phosphate 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 phosphates.") +AnnotationAssertion( "positive regulation of phosphate metabolism") +AnnotationAssertion( "up regulation of phosphate metabolic process") +AnnotationAssertion( "up-regulation of phosphate metabolic process") +AnnotationAssertion( "upregulation of phosphate metabolic process") +AnnotationAssertion( "activation of phosphate metabolic process") +AnnotationAssertion( "stimulation of phosphate metabolic process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045937") +AnnotationAssertion(rdfs:label "positive regulation of phosphate metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (negative regulation of steroid 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 steroids.") @@ -38245,6 +38909,17 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (heterocycle metabolic process) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).") +AnnotationAssertion( "heterocycle metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046483") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "heterocycle metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (photoreceptor cell differentiation) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "ISBN:0198506732") "The specialization of organization of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. An example of this process is found in Drosophila melanogaster.") @@ -39569,7 +40244,7 @@ SubClassOf( "GOC:jid") "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048583") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of response to stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -39585,7 +40260,7 @@ AnnotationAssertion( "stimulation of response to stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048584") -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 "positive regulation of response to stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -39601,7 +40276,7 @@ AnnotationAssertion( "inhibition of response to stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048585") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of response to stimulus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -39714,15 +40389,13 @@ SubClassOf( ObjectSomeValuesFrom( (multicellular organismal reproductive process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") Annotation( "GOC:tb") "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) AnnotationAssertion( "organismal reproductive process") AnnotationAssertion( "reproductive process in a multicellular organism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048609") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "multicellular organismal reproductive process") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (myoblast development) @@ -40415,7 +41088,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anatomical structure development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -40494,7 +41166,6 @@ SubClassOf( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:mlg") "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19809"^^xsd:anyURI) -AnnotationAssertion( ) AnnotationAssertion( "cell locomotion") AnnotationAssertion( "movement of a cell") AnnotationAssertion( "biological_process") @@ -40502,14 +41173,10 @@ AnnotationAssertion( "GO:0048870") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell motility") SubClassOf( ) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) -DisjointClasses( ObjectSomeValuesFrom( )) # Class: (multicellular organismal-level homeostasis) @@ -40531,6 +41198,15 @@ AnnotationAssertion( "homeostasis of number of cells") SubClassOf( ) +# Class: (chemical homeostasis) + +AnnotationAssertion(Annotation( "GOC:isa_complete") "Any biological process involved in the maintenance of an internal steady state of a chemical.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0048878") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "chemical homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (sensory system development) AnnotationAssertion(Annotation( "GOC:dgh") "The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure.") @@ -40908,6 +41584,19 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (regulation of catalytic activity) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:ebc") Annotation( "GOC:vw") "Any process that modulates the activity of an enzyme.") +AnnotationAssertion( "GO:0048552") +AnnotationAssertion( "regulation of enzyme activity") +AnnotationAssertion( "regulation of metalloenzyme activity") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0050790") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulation of catalytic activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of developmental process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).") @@ -40938,6 +41627,20 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (monoatomic ion homeostasis) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process involved in the maintenance of an internal steady state of monoatomic ions within an organism or cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) +AnnotationAssertion( "GO:2000021") +AnnotationAssertion( "ion homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "electrolyte homeostasis") +AnnotationAssertion( "negative regulation of crystal formation") +AnnotationAssertion( "regulation of ion homeostasis") +AnnotationAssertion( "GO:0050801") +AnnotationAssertion(rdfs:label "monoatomic ion homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of synapse structure or activity) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).") @@ -41050,15 +41753,11 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell activation) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050865") AnnotationAssertion(rdfs:label "regulation of cell activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) -DisjointClasses( ObjectSomeValuesFrom( )) # Class: (negative regulation of cell activation) @@ -41120,7 +41819,6 @@ SubClassOf( (musculoskeletal movement) AnnotationAssertion(Annotation( "GOC:dph") "The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050881") AnnotationAssertion(rdfs:label "musculoskeletal movement") @@ -41156,13 +41854,12 @@ AnnotationAssertion( "physiological response to stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050896") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) 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 stimulus") SubClassOf( ) @@ -41786,6 +42483,59 @@ AnnotationAssertion( "import into nucleus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +# Class: (regulation of nitrogen compound metabolic process) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") +AnnotationAssertion(Annotation( "GOC:tb") "regulation of nitrogen metabolic process") +AnnotationAssertion( "regulation of nitrogen metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051171") +AnnotationAssertion(rdfs:label "regulation of nitrogen compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (negative regulation of nitrogen compound metabolic process) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") +AnnotationAssertion( "down regulation of nitrogen metabolic process") +AnnotationAssertion( "down-regulation of nitrogen metabolic process") +AnnotationAssertion( "downregulation of nitrogen metabolic process") +AnnotationAssertion(Annotation( "GOC:tb") "negative regulation of nitrogen metabolic process") +AnnotationAssertion( "negative regulation of nitrogen metabolism") +AnnotationAssertion( "inhibition of nitrogen metabolic process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051172") +AnnotationAssertion(rdfs:label "negative regulation of nitrogen compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (positive regulation of nitrogen compound metabolic process) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") +AnnotationAssertion(Annotation( "GOC:tb") "positive regulation of nitrogen metabolic process") +AnnotationAssertion( "positive regulation of nitrogen metabolism") +AnnotationAssertion( "up regulation of nitrogen metabolic process") +AnnotationAssertion( "up-regulation of nitrogen metabolic process") +AnnotationAssertion( "upregulation of nitrogen metabolic process") +AnnotationAssertion( "activation of nitrogen metabolic process") +AnnotationAssertion( "stimulation of nitrogen metabolic process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051173") +AnnotationAssertion(rdfs:label "positive regulation of nitrogen compound metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (regulation of phosphorus metabolic process) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.") +AnnotationAssertion( "regulation of phosphorus metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051174") +AnnotationAssertion(rdfs:label "regulation of phosphorus metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (negative regulation of sulfur metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur.") @@ -41820,7 +42570,6 @@ EquivalentClasses( ObjectIntersection # Class: (localization) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dos") "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27052"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-18T13:51:04Z") AnnotationAssertion( "GO:1902578") @@ -41834,7 +42583,6 @@ AnnotationAssertion( "GOC:TermGenie") "single organism localization") AnnotationAssertion( "single-organism localization") AnnotationAssertion( "GO:0051179") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "localization") SubClassOf( ) @@ -42208,6 +42956,51 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) +# Class: (regulation of transferase activity) + +AnnotationAssertion(Annotation( "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( "biological_process") +AnnotationAssertion( "GO:0051338") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") +AnnotationAssertion(rdfs:label "regulation of transferase activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of transferase activity) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases 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 a donor compound to an acceptor.") +AnnotationAssertion( "transferase activator") +AnnotationAssertion( "up regulation of transferase activity") +AnnotationAssertion( "up-regulation of transferase activity") +AnnotationAssertion( "upregulation of transferase activity") +AnnotationAssertion( "activation of transferase activity") +AnnotationAssertion( "stimulation of transferase activity") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051347") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") +AnnotationAssertion(rdfs:label "positive regulation of transferase activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of transferase activity) + +AnnotationAssertion(Annotation( "GOC:ai") "Any process that stops or reduces the rate 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 a donor compound to an acceptor.") +AnnotationAssertion( "down regulation of transferase activity") +AnnotationAssertion( "down-regulation of transferase activity") +AnnotationAssertion( "downregulation of transferase activity") +AnnotationAssertion( "transferase inhibitor") +AnnotationAssertion( "inhibition of transferase activity") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051348") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.") +AnnotationAssertion(rdfs:label "negative regulation of transferase activity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (neuron apoptotic process) AnnotationAssertion(Annotation( "CL:0000540") Annotation( "GOC:mtg_apoptosis") "Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.") @@ -42536,7 +43329,6 @@ SubClassOf( ObjectAllValuesFrom( (cellular localization) AnnotationAssertion(Annotation( "GOC:tb") Annotation( "GOC:vw") "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-18T14:04:32Z") AnnotationAssertion( "GO:1902580") @@ -42549,9 +43341,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism cellular localization") AnnotationAssertion( "GO:0051641") -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 "cellular localization") SubClassOf( ) SubClassOf( ) @@ -42761,7 +43551,7 @@ SubClassOf( "GOC:bf") Annotation( "GOC:jl") "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. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051716") -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 "cellular response to stimulus") SubClassOf( ) @@ -43035,8 +43825,6 @@ AnnotationAssertion( "regulation of nervous system development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) # Class: (negative regulation of nervous system development) @@ -43451,6 +44239,48 @@ AnnotationAssertion(rdfs:label "asym EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (phosphate ion homeostasis) + +AnnotationAssertion(Annotation( "GOC:jid") Annotation( "GOC:mah") "Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26429"^^xsd:anyURI) +AnnotationAssertion( "phosphate homeostasis") +AnnotationAssertion( "Pi homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0055062") +AnnotationAssertion(rdfs:label "phosphate ion homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (sulfate ion homeostasis) + +AnnotationAssertion(Annotation( "GOC:jid") Annotation( "GOC:mah") "Any process involved in the maintenance of an internal steady state of sulfate ions within an organism or cell.") +AnnotationAssertion( "GO:0080174") +AnnotationAssertion( "sulfate homeostasis") +AnnotationAssertion( "sulphate ion homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0055063") +AnnotationAssertion(rdfs:label "sulfate ion homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (monoatomic cation homeostasis) + +AnnotationAssertion(Annotation( "GOC:ceb") Annotation( "GOC:jid") Annotation( "GOC:mah") "Any process involved in the maintenance of an internal steady state of monoatomic cations within an organism or cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) +AnnotationAssertion( "cation homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0055080") +AnnotationAssertion(rdfs:label "monoatomic cation homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (intracellular chemical homeostasis) + +AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:jid") "A homeostatic process involved in the maintenance of a steady state level of a chemical within a cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24514"^^xsd:anyURI) +AnnotationAssertion( "cellular chemical homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0055082") +AnnotationAssertion(rdfs:label "intracellular chemical homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (transmembrane transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.") @@ -43463,7 +44293,6 @@ AnnotationAssertion( "GO:0055085") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -43488,6 +44317,14 @@ AnnotationAssertion(rdfs:label "nucl SubClassOf( ) SubClassOf( ) +# Class: (lipid homeostasis) + +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:rl") "Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0055088") +AnnotationAssertion(rdfs:label "lipid homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (Golgi to secretory granule transport) AnnotationAssertion(Annotation( "GOC:curators") "The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bounded particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex.") @@ -44084,6 +44921,16 @@ AnnotationAssertion(rdfs:label "cran EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (regulation of brood size) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates brood size. Brood size is the number of progeny that survive embryogenesis and are cared for at one time.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0060378") +AnnotationAssertion(rdfs:label "regulation of brood size") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (cardiac muscle cell myoblast differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which a relatively unspecialized cell acquires specialized features of a cardiac myoblast. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life.") @@ -45338,8 +46185,6 @@ AnnotationAssertion( "GO:0060998") AnnotationAssertion(rdfs:label "regulation of dendritic spine development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) # Class: (positive regulation of dendritic spine development) @@ -46484,6 +47329,17 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (transferase complex, transferring phosphorus-containing groups) + +AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "GOC:dph") "A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") +AnnotationAssertion( "dph") +AnnotationAssertion( "2015-05-06T11:22:38Z") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0061695") +AnnotationAssertion(rdfs:label "transferase complex, transferring phosphorus-containing groups") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (secretory granule maturation) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "GOC:dph") Annotation( "PMID:16618809") "Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodeling.") @@ -46744,6 +47600,19 @@ AnnotationAssertion( "biological regulation") SubClassOf( ) +# Class: (regulation of molecular function) + +AnnotationAssertion(Annotation( "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( "biological_process") +AnnotationAssertion( "GO:0065009") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulation of molecular function") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (extracellular membrane-bounded organelle) AnnotationAssertion(Annotation( "GOC:isa_complete") "Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell.") @@ -47380,7 +48249,6 @@ AnnotationAssertion( "2010-03-08T03:56:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071705") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nitrogen compound transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -47481,7 +48349,6 @@ EquivalentClasses( ObjectIntersection # 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.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-10T01:39:16Z") AnnotationAssertion( "GO:0071841") @@ -47490,10 +48357,8 @@ AnnotationAssertion(Annotation( "cellular component organization or biogenesis at cellular level") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071840") -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 "cellular component organization or biogenesis") SubClassOf( ) @@ -47923,12 +48788,24 @@ AnnotationAssertion( "2009-05-06T04:51:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0080134") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of response to stress") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (intracellular amino acid homeostasis) + +AnnotationAssertion(Annotation( "PMID:19955263") "A homeostatic process involved in the maintenance of a steady state level of amino acids within a cell.") +AnnotationAssertion( "dhl") +AnnotationAssertion( "2010-01-27T04:47:27Z") +AnnotationAssertion( "amino acid homeostasis") +AnnotationAssertion( "cellular amino acid homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0080144") +AnnotationAssertion(rdfs:label "intracellular amino acid homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of fertilization) AnnotationAssertion(Annotation( "GOC:DHL") Annotation( "PMID:20478994") "Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).") @@ -48119,7 +48996,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0089718") AnnotationAssertion(rdfs:label "amino acid import across plasma membrane") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (positive regulation of microtubule nucleation) @@ -48419,13 +49296,10 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any cellular metabolic process involving nucleic acids.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26133"^^xsd:anyURI) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27052"^^xsd:anyURI) AnnotationAssertion( "tb") AnnotationAssertion( "2010-04-07T10:18:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090304") -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 "nucleic acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -48508,6 +49382,26 @@ AnnotationAssertion(rdfs:label "RNA EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (positive regulation of brood size) + +AnnotationAssertion(Annotation( "GOC:rz") "Any process that increases brood size. Brood size is the number of progeny that survive embryogenesis and are cared for at one time.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2016-12-19T15:07:32Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0090727") +AnnotationAssertion(rdfs:label "positive regulation of brood size") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of brood size) + +AnnotationAssertion(Annotation( "GOC:rz") "Any process that decreases brood size. Brood size is the number of progeny that survive embryogenesis and are cared for at one time.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2016-12-19T15:07:32Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0090728") +AnnotationAssertion(rdfs:label "negative regulation of brood size") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (pigment granule membrane) AnnotationAssertion(Annotation( "PMID:11294610") "Any membrane that is part of a pigment granule.") @@ -48640,7 +49534,7 @@ AnnotationAssertion( "GO:0097164") AnnotationAssertion(rdfs:label "ammonium ion metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) # Class: (apoptotic signaling pathway) @@ -48683,6 +49577,30 @@ AnnotationAssertion(rdfs:label "olig EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (ammonium homeostasis) + +AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:12695560") "Any biological process involved in the maintenance of an internal steady state of ammonium.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2012-03-22T02:51:22Z") +AnnotationAssertion( "ammonia homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0097272") +AnnotationAssertion(rdfs:label "ammonium homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (intracellular ammonium homeostasis) + +AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:12695560") "A homeostatic process involved in the maintenance of a steady state level of ammonium within a cell.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2012-03-22T02:54:38Z") +AnnotationAssertion( "cellular ammonia homeostasis") +AnnotationAssertion( "cellular ammonium homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0097275") +AnnotationAssertion(rdfs:label "intracellular ammonium homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (protein localization to heterochromatin) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin.") @@ -48969,7 +49887,7 @@ AnnotationAssertion( AnnotationAssertion( "region of plasma membrane") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098590") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.") AnnotationAssertion(rdfs:label "plasma membrane region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -49026,6 +49944,17 @@ EquivalentClasses( ObjectIntersection SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (monoatomic cation transmembrane transport) + +AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:vw") "The process in which a monoatomic cation is transported across a membrane. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom.") +AnnotationAssertion( "GO:0099132") +AnnotationAssertion( "cation transmembrane transport") +AnnotationAssertion( "ATP hydrolysis coupled cation transmembrane transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098655") +AnnotationAssertion(rdfs:label "monoatomic cation transmembrane transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (import into cell) AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.") @@ -49148,6 +50077,16 @@ AnnotationAssertion(rdfs:label "bone EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (inorganic ion homeostasis) + +AnnotationAssertion(Annotation( "GOC:dos") "Any process involved in the maintenance of an internal steady state of inorganic ions within an organism or cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24455"^^xsd:anyURI) +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0098771") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "inorganic ion homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (skin epidermis development) AnnotationAssertion(Annotation( "GOC:dos") "The process whose specific outcome is the progression of the skin epidermis over time, from its formation to the mature structure.") @@ -49567,7 +50506,7 @@ AnnotationAssertion( "GO:0099082") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retrograde trans-synaptic signaling by neuropeptide") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (retrograde trans-synaptic signaling by neuropeptide, modulating synaptic transmission) @@ -49577,7 +50516,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua.") AnnotationAssertion(rdfs:label "retrograde trans-synaptic signaling by neuropeptide, modulating synaptic transmission") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (microtubule polymerization based movement) @@ -49914,7 +50853,7 @@ AnnotationAssertion( "GO:0099538") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "synaptic signaling via neuropeptide") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (trans-synaptic signaling by neuropeptide) @@ -49923,7 +50862,7 @@ AnnotationAssertion( "GO:0099540") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "trans-synaptic signaling by neuropeptide") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (trans-synaptic signaling by lipid) @@ -49964,7 +50903,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua.") AnnotationAssertion(rdfs:label "trans-synaptic signaling by neuropeptide, modulating synaptic transmission") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (trans-synaptic signaling by lipid, modulating synaptic transmission) @@ -50299,7 +51238,6 @@ AnnotationAssertion(Annotation( "kmv") AnnotationAssertion( "2018-01-29T14:46:52Z") AnnotationAssertion( "biological_process") -AnnotationAssertion( "endosomal trafficking") AnnotationAssertion( "GO:0110077") AnnotationAssertion(rdfs:label "vesicle-mediated intercellular transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -50737,6 +51675,57 @@ AnnotationAssertion(rdfs:label "orga SubClassOf( ) SubClassOf( ) +# Class: (catalytic activity, acting on a protein) + +AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify a protein.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2017-09-14T10:32:59Z") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0140096") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "catalytic activity, acting on a protein") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (catalytic activity, acting on DNA) + +AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify DNA.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2017-09-14T12:03:51Z") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0140097") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "catalytic activity, acting on DNA") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (catalytic activity, acting on RNA) + +AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21612"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2017-09-14T12:05:21Z") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0140098") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "catalytic activity, acting on RNA") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (catalytic activity, acting on a glycoprotein) + +AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalysis of a biochemical reaction at physiological temperatures in which one of the substrates is a glycoprotein.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2017-09-15T19:27:54Z") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0140103") +AnnotationAssertion(rdfs:label "catalytic activity, acting on a glycoprotein") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # 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.") @@ -50937,6 +51926,18 @@ AnnotationAssertion(rdfs:label "vacu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (catalytic activity, acting on a nucleic acid) + +AnnotationAssertion(Annotation( "GOC:pg") "Catalytic activity that acts to modify a nucleic acid.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21402"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2021-05-11T06:31:07Z") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0140640") +AnnotationAssertion(rdfs:label "catalytic activity, acting on a nucleic acid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (radial glia-guided pyramidal neuron migration) AnnotationAssertion(Annotation( "PMID:3760547") "The radial migration of a pyramidal neuron along radial glial cells.") @@ -50975,31 +51976,31 @@ AnnotationAssertion( "cytosol to Golgi apparatus transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -# Class: (nucleic acid biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The biosynthetic process resulting in the formation of a nucleic acid.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27408"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2024-03-25T07:33:40Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0141187") -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 "nucleic acid biosynthetic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (nucleic acid catabolic process) - -AnnotationAssertion(Annotation( "GOC:curators") "The cellular DNA metabolic process resulting in the breakdown of a nucleic acid.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27408"^^xsd:anyURI) -AnnotationAssertion( "pg") -AnnotationAssertion( "2024-03-25T07:35:06Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0141188") -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 "nucleic acid catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (multicellular organismal-level chemical homeostasis) + +AnnotationAssertion(Annotation( "GOC:curators") "A homeostatic process involved in the maintenance of a steady state level of a chemical within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24554"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2022-12-12T09:11:06Z") +AnnotationAssertion( "multicellular organism level chemical homeostasis") +AnnotationAssertion( "organismal level chemical homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0140962") +AnnotationAssertion(rdfs:label "multicellular organismal-level chemical homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (intracellular nitrogen homeostasis) + +AnnotationAssertion(Annotation( "GOC:tb") "A homeostatic process involved in the maintenance of a steady state level of nitrogen within a cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25558"^^xsd:anyURI) +AnnotationAssertion( "pg") +AnnotationAssertion( "2023-06-15T08:56:16Z") +AnnotationAssertion( "cellular nitrogen homeostasis") +AnnotationAssertion( "nitrogen homeostasis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0141067") +AnnotationAssertion(rdfs:label "intracellular nitrogen homeostasis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (regulation of postsynapse assembly) @@ -52463,12 +53464,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organonitrogen compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +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( "pr") AnnotationAssertion( "2012-11-04T15:18:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound anabolism") @@ -52477,7 +53478,6 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901566") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organonitrogen compound biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -52486,7 +53486,6 @@ SubClassOf( (organic substance biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-05T11:04:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity anabolism") @@ -52500,7 +53499,6 @@ AnnotationAssertion( "organic substance synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901576") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic substance biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -52646,7 +53644,7 @@ AnnotationAssertion( AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901652") AnnotationAssertion(rdfs:label "response to peptide") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (response to ketone) @@ -52705,28 +53703,22 @@ SubClassOf( (response to nitrogen compound) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "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 nitrogen compound stimulus.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:06:08Z") AnnotationAssertion( "response to nitrogen molecular entity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901698") -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 nitrogen compound") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (response to oxygen-containing compound) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "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 oxygen-containing compound stimulus.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:11:37Z") AnnotationAssertion( "response to oxygen molecular entity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901700") -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 oxygen-containing compound") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -53017,7 +54009,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cilium assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:dph") Annotation( "PMID:17719545") "Any process that modulates the frequency, rate or extent of cilium assembly.") -AnnotationAssertion( ) AnnotationAssertion( "dph") AnnotationAssertion( "2013-03-26T18:10:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ciliogenesis") @@ -53026,9 +54017,6 @@ AnnotationAssertion(Annotation( "GO:1902017") AnnotationAssertion(rdfs:label "regulation of cilium assembly") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) -DisjointClasses( ObjectSomeValuesFrom( )) # Class: (negative regulation of cilium assembly) @@ -53688,6 +54676,19 @@ AnnotationAssertion( "positive regulation of protein localization to synapse") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (catalytic complex) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "PMID:8077207") "A protein complex which is capable of catalytic activity.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19980"^^xsd:anyURI) +AnnotationAssertion( "bhm") +AnnotationAssertion( "2013-11-13T16:18:47Z") +AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "GOC:jl") "enzyme complex") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:1902494") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "catalytic complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of organelle transport along microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "PMID:21147087") "Any process that modulates the frequency, rate or extent of organelle transport along microtubule.") @@ -56082,6 +57083,45 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (regulation of monoatomic cation transmembrane transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15304482") "Any process that modulates the frequency, rate or extent of cation transmembrane transport.") +AnnotationAssertion( "sl") +AnnotationAssertion( "2015-03-18T21:11:43Z") +AnnotationAssertion( "regulation of cation transmembrane transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904062") +AnnotationAssertion(rdfs:label "regulation of monoatomic cation transmembrane transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of cation transmembrane transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15304482") "Any process that stops, prevents or reduces the frequency, rate or extent of cation transmembrane transport.") +AnnotationAssertion( "sl") +AnnotationAssertion( "2015-03-18T21:11:50Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cation transmembrane transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cation transmembrane transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cation transmembrane transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cation transmembrane transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904063") +AnnotationAssertion(rdfs:label "negative regulation of cation transmembrane transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of cation transmembrane transport) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15304482") "Any process that activates or increases the frequency, rate or extent of cation transmembrane transport.") +AnnotationAssertion( "sl") +AnnotationAssertion( "2015-03-18T21:11:55Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cation transmembrane transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cation transmembrane transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cation transmembrane transport") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cation transmembrane transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904064") +AnnotationAssertion(rdfs:label "positive regulation of cation transmembrane transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of trophectodermal cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24508636") "Any process that modulates the frequency, rate or extent of trophectodermal cell proliferation.") @@ -57839,6 +58879,18 @@ AnnotationAssertion( "positive regulation of endothelial cell activation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (transmembrane phosphate ion transport from cytosol to vacuole) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000078") Annotation( "PMID:26554016") "The directed movement of phosphate ions from the cytosol across the vacuolar membrane and into the vacuolar lumen.") +AnnotationAssertion( "tb") +AnnotationAssertion( "2016-03-03T00:34:12Z") +AnnotationAssertion( "GO:0007037") +AnnotationAssertion( "vacuolar phosphate transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905011") +AnnotationAssertion(rdfs:label "transmembrane phosphate ion transport from cytosol to vacuole") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + # Class: (carboxylic acid transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000069") Annotation( "PMID:10869563") "The process in which carboxylic acid is transported across a membrane.") @@ -60241,6 +61293,16 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses( ObjectSomeValuesFrom( )) +# Class: (transferase complex) + +AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:16540464") "A protein complex capable of catalyzing 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).") +AnnotationAssertion( "bhm") +AnnotationAssertion( "2013-11-12T13:20:12Z") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:1990234") +AnnotationAssertion(rdfs:label "transferase complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (RNA localization to chromatin) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:mah") Annotation( "PMID:22582262") "A process in which RNA is transported to and maintained in a part of a chromosome that is organized into chromatin.") @@ -60609,6 +61671,39 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (regulation of phosphate transmembrane transport) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of phosphate transmembrane transport.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2010-10-15T11:33:04Z") +AnnotationAssertion( "regulation of phosphate membrane transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2000185") +AnnotationAssertion(rdfs:label "regulation of phosphate transmembrane transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (negative regulation of phosphate transmembrane transport) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents, or reduces the frequency, rate or extent of phosphate transmembrane transport.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2010-10-15T11:33:08Z") +AnnotationAssertion( "negative regulation of phosphate membrane transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2000186") +AnnotationAssertion(rdfs:label "negative regulation of phosphate transmembrane transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (positive regulation of phosphate transmembrane transport) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of phosphate transmembrane transport.") +AnnotationAssertion( "vw") +AnnotationAssertion( "2010-10-15T11:33:10Z") +AnnotationAssertion( "positive regulation of phosphate membrane transport") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2000187") +AnnotationAssertion(rdfs:label "positive regulation of phosphate transmembrane transport") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (regulation of female gonad development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of female gonad development.") @@ -61739,7 +62834,6 @@ SubClassOf(Annotation( (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( ) AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-24T01:20:58Z") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of apoptotic signalling pathway") @@ -61747,10 +62841,7 @@ AnnotationAssertion( "GO:2001235") AnnotationAssertion(rdfs:label "positive regulation of apoptotic signaling pathway") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -DisjointClasses( ObjectSomeValuesFrom( )) # Class: (negative regulation of chromosome organization) @@ -62670,7 +63761,6 @@ SubClassOf( (Saccharomyces cerevisiae) AnnotationAssertion( ) -AnnotationAssertion( "NCBITaxon:2898199") AnnotationAssertion( "NCBITaxon:41870") AnnotationAssertion( "GC_ID:1") AnnotationAssertion(Annotation( ) "Saccharomyces cerevisiae 'var. diastaticus'") @@ -63036,7 +64126,7 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "protein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -63485,20 +64575,20 @@ EquivalentClasses( ObjectIntersecti SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (protein-containing molecular entity) - -AnnotationAssertion(Annotation( "PRO:DAN") "A molecular entity that minimally consists of a protein.") -AnnotationAssertion(Annotation( "PRO:DAN") "protein") -AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") -AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") -AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") -AnnotationAssertion( "protein") -AnnotationAssertion( "PR:000064867") -AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565).") -AnnotationAssertion(rdfs:label "protein-containing molecular entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing material entity) + +AnnotationAssertion(Annotation( "PRO:DAN") "A material entity that minimally consists of a protein.") +AnnotationAssertion(Annotation( "PRO:DAN") "protein") +AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") +AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") +AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000050567") +AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).") +AnnotationAssertion(rdfs:label "protein-containing material entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (T-cell surface glycoprotein CD8 alpha chain (mouse)) @@ -64123,6 +65213,7 @@ AnnotationAssertion( "zone of skin") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -64473,6 +65564,7 @@ AnnotationAssertion( "serous membrane") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -64624,6 +65716,7 @@ AnnotationAssertion(Annotation( "UBERON:0000058") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "duct") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -65144,6 +66237,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0000094") AnnotationAssertion(rdfs:label "membrane organ") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA-def") ObjectSomeValuesFrom( )) @@ -65470,6 +66564,7 @@ AnnotationAssertion( "UBERON:0000117") AnnotationAssertion(rdfs:label "respiratory tube") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -65826,6 +66921,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "CL:tm") ObjectSomeValuesFrom( )) @@ -65898,6 +66994,7 @@ AnnotationAssertion(Annotation( "UBERON:0000304") AnnotationAssertion(rdfs:label "tendon sheath") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -66009,6 +67106,7 @@ AnnotationAssertion( "mucosa") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png"^^xsd:anyURI) AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -66977,6 +68075,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -67946,6 +69045,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cornea") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) @@ -68354,10 +69454,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reproductive system") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg"^^xsd:anyURI) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -68386,6 +69486,7 @@ AnnotationAssertion( "BSA:0000079") AnnotationAssertion( "BTO:0000534") AnnotationAssertion( "EMAPA:17383") +AnnotationAssertion(Annotation( ) "FBbt:00004858") AnnotationAssertion( "FMA:18250") AnnotationAssertion( "GAID:368") AnnotationAssertion( "HAO:0000379") @@ -73325,6 +74426,7 @@ AnnotationAssertion( "capsule of lens") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -74219,6 +75321,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood plasma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -74486,6 +75589,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "blood vessel") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -75222,6 +76326,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dermis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -75269,6 +76374,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hypodermis") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "ZFA") ObjectSomeValuesFrom( )) @@ -75802,6 +76908,7 @@ AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_M_Skin.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -76385,6 +77492,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "integument") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -77202,6 +78310,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "exocrine system") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -77812,6 +78921,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "exocrine gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -78315,6 +79425,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pericardium") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "MA") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -78461,6 +79572,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "integumental system") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -78951,6 +80063,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tunica intima") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf(Annotation( "check for exceptions, e.g. capillaries") ObjectSomeValuesFrom( )) @@ -80739,10 +81852,10 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "reproductive organ") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (female reproductive organ) @@ -85960,6 +87073,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cardiovascular system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -85983,6 +87097,7 @@ AnnotationAssertion(rdfs:label " AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"^^xsd:anyURI) AnnotationAssertion( "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -86063,6 +87178,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arterial system") +SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -86117,6 +87233,7 @@ AnnotationAssertion( "UBERON:0004582") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "venous system") +SubClassOf( ) SubClassOf(Annotation( "MA") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -86428,6 +87545,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "paired limb/fin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(Annotation( "VSAO") ) SubClassOf(Annotation( "VSAO") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -89429,6 +90547,7 @@ AnnotationAssertion(Annotation( "UBERON:0005734") AnnotationAssertion(rdfs:label "tunica adventitia of blood vessel") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg"^^xsd:anyURI) +SubClassOf( ) SubClassOf(Annotation( "cjm") ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -89523,6 +90642,7 @@ AnnotationAssertion( "FMA:63872") "basement membrane") AnnotationAssertion( "UBERON:0005769") AnnotationAssertion(rdfs:label "basement membrane of epithelium") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -89772,6 +90892,7 @@ AnnotationAssertion( "UBERON:0005906") AnnotationAssertion(rdfs:comment "See notes for serous membrane") AnnotationAssertion(rdfs:label "serous sac") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -91268,6 +92389,7 @@ AnnotationAssertion( "UBERON:0006965") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vascular cord") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -91647,6 +92769,7 @@ AnnotationAssertion( "UBERON:0007195") AnnotationAssertion(rdfs:label "stroma of bone marrow") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -92774,6 +93897,7 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0007845") AnnotationAssertion(rdfs:label "regular connective tissue") +SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -93122,6 +94246,7 @@ AnnotationAssertion( "UBERON:0008886") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary vascular system") +SubClassOf( ) SubClassOf(Annotation( "Obol") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -95515,6 +96640,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "meningeal cluster") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -95786,6 +96912,7 @@ AnnotationAssertion( "UBERON:0011234") AnnotationAssertion(rdfs:label "fibrous membrane of synovial tendon sheath") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -96222,6 +97349,7 @@ AnnotationAssertion( "UBERON:0011823") AnnotationAssertion(rdfs:label "dense connective tissue") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -96271,6 +97399,7 @@ AnnotationAssertion( "UBERON:0011860") AnnotationAssertion(rdfs:label "collection of collagen fibrils") AnnotationAssertion(rdfs:seeAlso ) +SubClassOf( ) SubClassOf(Annotation( "ZFA") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -96458,6 +97587,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stomach glandular region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -96756,6 +97886,7 @@ AnnotationAssertion(Annotation( "Wikipedia:Fibrous_tunic_of_eyeball") "fibrous tunic") AnnotationAssertion( "UBERON:0012430") AnnotationAssertion(rdfs:label "tunica fibrosa of eyeball") +SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "FMA") ) SubClassOf( ) @@ -99103,6 +100234,7 @@ AnnotationAssertion(Annotation( "uberon") AnnotationAssertion( "UBERON:0034929") AnnotationAssertion(rdfs:label "external soft tissue zone") +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -100256,8 +101388,6 @@ SubClassOf( ObjectSomeValuesFrom( SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ) SubClassOf(Annotation( ) ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -100313,6 +101443,7 @@ SubClassOf(ObjectIntersectionOf( SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) @@ -100360,7 +101491,12 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -100382,9 +101518,35 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -100393,8 +101555,38 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file From 48cb964d41c0cbf9cfc2bbd09312750010b1d6b3 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 10 Aug 2024 09:45:04 +0300 Subject: [PATCH 3/4] Register PATO to QUDT mapping in config --- src/ontology/pato-odk.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/ontology/pato-odk.yaml b/src/ontology/pato-odk.yaml index fdd4a44..aafcc5b 100644 --- a/src/ontology/pato-odk.yaml +++ b/src/ontology/pato-odk.yaml @@ -77,4 +77,8 @@ robot_report: - orcid-contributor - iri-range custom_sparql_exports : - - basic-report \ No newline at end of file + - basic-report +sssom_mappingset_group: + products: + - id: pato-to-qudt-quantitykind + maintenance: manual From 8b8360cfa60e62d1b5aa78f41607acfed87a7e7f Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 10 Aug 2024 09:45:22 +0300 Subject: [PATCH 4/4] Refresh ODK (includes 1.5.2 migration) --- .github/workflows/qc.yml | 6 +- docs/odk-workflows/ManageDocumentation.md | 1 + docs/odk-workflows/RepoManagement.md | 2 +- src/ontology/Makefile | 164 +++++++++++++++------- src/ontology/run.sh | 38 ++++- src/scripts/run-command.sh | 4 + src/scripts/update_repo.sh | 5 +- src/sparql/class-count-by-prefix.sparql | 2 +- 8 files changed, 163 insertions(+), 59 deletions(-) create mode 100755 src/scripts/run-command.sh diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 21966a7..ec0efec 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,15 +19,15 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.3.0 + container: obolibrary/odkfull:v1.5.2 # Steps represent a sequence of tasks that will be executed as part of the job steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Run ontology QC checks env: DEFAULT_BRANCH: master - run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false + run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false diff --git a/docs/odk-workflows/ManageDocumentation.md b/docs/odk-workflows/ManageDocumentation.md index 7840c1f..17f986a 100644 --- a/docs/odk-workflows/ManageDocumentation.md +++ b/docs/odk-workflows/ManageDocumentation.md @@ -44,3 +44,4 @@ The documentation is _not_ automatically updated from the Markdown, and needs to Just make sure you give GitHub 2-5 minutes to build the pages! + diff --git a/docs/odk-workflows/RepoManagement.md b/docs/odk-workflows/RepoManagement.md index 2934798..4e4082b 100644 --- a/docs/odk-workflows/RepoManagement.md +++ b/docs/odk-workflows/RepoManagement.md @@ -2,7 +2,7 @@ ## Updating your ODK repository -Your ODK repositories configuration is managed in `src/ontology/pato-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository: +Your ODK repositories configuration is managed in `src/ontology/pato-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository: ``` diff --git a/src/ontology/Makefile b/src/ontology/Makefile index a898f8a..47e4491 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for pato # Generated using ontology-development-kit -# ODK Version: v1.4 +# ODK Version: v1.5.2 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use pato.Makefile instead @@ -9,6 +9,9 @@ # ---------------------------------------- # More information: https://github.com/INCATools/ontology-development-kit/ +# Fingerprint of the configuration file when this Makefile was last generated +CONFIG_HASH= 8c38f556f1076ce2a46088cd083451de27b8553932affe92d72c22f02b6e92e4 + # ---------------------------------------- # Standard Constants @@ -44,7 +47,7 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE) OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference properties-as-annotation-and-object missing-label illegal-annotation-property orcid-contributor iri-range SPARQL_EXPORTS = basic-report -ODK_VERSION_MAKEFILE = v1.4 +ODK_VERSION_MAKEFILE = v1.5.2 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -59,6 +62,11 @@ FORMATS = $(sort owl obo json owl) FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-simple $(ONT)-full ) +ifeq ($(ODK_DEBUG),yes) +ODK_DEBUG_FILE = debug.log +SHELL = $(SCRIPTSDIR)/run-command.sh +endif + # ---------------------------------------- # Top-level targets # ---------------------------------------- @@ -69,12 +77,16 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-simple $(ONT)-full ) all: all_odk .PHONY: all_odk -all_odk: odkversion test all_assets +all_odk: odkversion config_check test custom_reports all_assets .PHONY: test test: odkversion reason_test sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt echo "Finished running all tests successfully." +.PHONY: test +test_fast: + $(MAKE_FAST) test + .PHONY: release_diff release_diff: $(REPORTDIR)/release-diff.md @@ -85,13 +97,52 @@ reason_test: $(EDIT_PREPROCESSED) .PHONY: odkversion odkversion: - echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, \ - not the version of the ODK you are running)" &&\ - echo "ROBOT version (ODK): " && $(ROBOT) --version + @echo "ODK Makefile $(ODK_VERSION_MAKEFILE)" + @odk-info --tools +.PHONY: config_check +config_check: + @if [ "$$(sha256sum $(ONT)-odk.yaml | cut -c1-64)" = "$(CONFIG_HASH)" ]; then \ + echo "Repository is up-to-date." ; else \ + echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'make update_repo'." ; fi + $(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR): mkdir -p $@ +# ---------------------------------------- +# ODK-managed ROBOT plugins +# ---------------------------------------- + +# Make sure ROBOT knows where to find plugins +export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins + +# Override this rule in pato.Makefile to install custom plugins +.PHONY: custom_robot_plugins +custom_robot_plugins: + + +.PHONY: extra_robot_plugins +extra_robot_plugins: + + +# Install all ROBOT plugins to the runtime plugins directory +.PHONY: all_robot_plugins +all_robot_plugins: $(foreach plugin,$(notdir $(wildcard /tools/robot-plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + custom_robot_plugins extra_robot_plugins \ + +# Default rule to install plugins +$(ROBOT_PLUGINS_DIRECTORY)/%.jar: + @mkdir -p $(ROBOT_PLUGINS_DIRECTORY) + @if [ -f ../../plugins/$*.jar ]; then \ + ln ../../plugins/$*.jar $@ ; \ + elif [ -f /tools/robot-plugins/$*.jar ]; then \ + cp /tools/robot-plugins/$*.jar $@ ; \ + fi + +# Specific rules for supplementary plugins defined in configuration + + # ---------------------------------------- # Release assets # ---------------------------------------- @@ -137,7 +188,7 @@ all_subsets: $(SUBSET_FILES) # ---------------------------------------- -MAPPINGS = +MAPPINGS = pato-to-qudt-quantitykind MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS)) @@ -181,12 +232,12 @@ validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) -sparql_test: $(EDIT_PREPROCESSED) pato-base.owl catalog-v001.xml | $(REPORTDIR) +sparql_test: $(EDIT_PREPROCESSED) pato-base.owl | $(REPORTDIR) ifneq ($(SPARQL_VALIDATION_QUERIES),) - $(ROBOT) verify --catalog catalog-v001.xml -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) + $(ROBOT) verify -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) - $(ROBOT) verify --catalog catalog-v001.xml -i pato-base.owl --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) + $(ROBOT) verify -i pato-base.owl --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) endif # ---------------------------------------- @@ -199,6 +250,14 @@ $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR) $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR) $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri http://purl.obolibrary.org/obo/PATO_ --base-iri http://purl.obolibrary.org/obo/pato# --print 5 -o $@ +check_for_robot_updates: + @cut -f2 "/tools/robot_report_profile.txt" | sort > $(TMPDIR)/sorted_tsv2.txt + @cut -f2 "$(ROBOT_PROFILE)" | sort > $(TMPDIR)/sorted_tsv1.txt + @comm -23 $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/sorted_tsv1.txt > $(TMPDIR)/missing.txt + @echo "Missing tests:" + @cat $(TMPDIR)/missing.txt + @rm $(TMPDIR)/sorted_tsv1.txt $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/missing.txt $(TMPDIR)/report_profile_robot.txt + # ---------------------------------------- # Release assets # ---------------------------------------- @@ -215,7 +274,7 @@ RELEASE_ASSETS = \ $(SUBSET_FILES) .PHONY: all_assets -all_assets: $(ASSETS) +all_assets: $(ASSETS) check_rdfxml_assets .PHONY: show_assets show_assets: @@ -223,7 +282,7 @@ show_assets: du -sh $(ASSETS) check_rdfxml_%: % - @check-rdfxml $< + @check-rdfxml $< .PHONY: check_rdfxml_assets check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl) @@ -318,6 +377,7 @@ $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_term if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \ 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 \ $(ANNOTATE_CONVERT_FILE); fi @@ -380,9 +440,9 @@ recreate-%: no-mirror-recreate-%: $(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B -$(COMPONENTSDIR)/%: | $(COMPONENTSDIR) - touch $@ -.PRECIOUS: $(COMPONENTSDIR)/% +$(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR) + test -f $@ || touch $@ +.PRECIOUS: $(COMPONENTSDIR)/%.owl # ---------------------------------------- @@ -393,87 +453,87 @@ IMP=true # Global parameter to bypass import generation MIR=true # Global parameter to bypass mirror generation IMP_LARGE=true # Global parameter to bypass handling of large imports +ifeq ($(strip $(MIR)),true) ## ONTOLOGY: ro .PHONY: mirror-ro .PRECIOUS: $(MIRRORDIR)/ro.owl mirror-ro: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 400 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 400 && \ + $(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: chebi .PHONY: mirror-chebi .PRECIOUS: $(MIRRORDIR)/chebi.owl mirror-chebi: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CHEBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + $(ROBOT) remove -I https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl --base-iri $(OBOBASE)/CHEBI --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ## ONTOLOGY: go .PHONY: mirror-go .PRECIOUS: $(MIRRORDIR)/go.owl mirror-go: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/go/go-base.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 400 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/go/go-base.owl --create-dirs -o $(TMPDIR)/go-download.owl --retry 4 --max-time 400 && \ + $(ROBOT) convert -i $(TMPDIR)/go-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: pco .PHONY: mirror-pco .PRECIOUS: $(MIRRORDIR)/pco.owl mirror-pco: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pco.owl --create-dirs -o $(MIRRORDIR)/pco.owl --retry 4 --max-time 400 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/pco.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PCO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/pco.owl --create-dirs -o $(TMPDIR)/pco-download.owl --retry 4 --max-time 400 && \ + $(ROBOT) remove -i $(TMPDIR)/pco-download.owl --base-iri $(OBOBASE)/PCO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ## ONTOLOGY: uberon .PHONY: mirror-uberon .PRECIOUS: $(MIRRORDIR)/uberon.owl mirror-uberon: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/uberon/uberon-base.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 400 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/uberon/uberon-base.owl --create-dirs -o $(TMPDIR)/uberon-download.owl --retry 4 --max-time 400 && \ + $(ROBOT) convert -i $(TMPDIR)/uberon-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: cl .PHONY: mirror-cl .PRECIOUS: $(MIRRORDIR)/cl.owl mirror-cl: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cl/cl-base.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 400 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/cl/cl-base.owl --create-dirs -o $(TMPDIR)/cl-download.owl --retry 4 --max-time 400 && \ + $(ROBOT) convert -i $(TMPDIR)/cl-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: ncbitaxon .PHONY: mirror-ncbitaxon .PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl mirror-ncbitaxon: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: pr .PHONY: mirror-pr .PRECIOUS: $(MIRRORDIR)/pr.owl mirror-pr: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PR --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + $(ROBOT) remove -I https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl --base-iri $(OBOBASE)/PR --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS)) MERGE_MIRRORS = true +ifeq ($(strip $(MERGE_MIRRORS)),true) $(MIRRORDIR)/merged.owl: $(ALL_MIRRORS) - if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(ROBOT) merge $(patsubst %, -i %, $^) -o $@; fi + $(ROBOT) merge $(patsubst %, -i %, $^) -o $@ .PRECIOUS: $(MIRRORDIR)/merged.owl +endif $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) - if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ + if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi +else # MIR=false +$(MIRRORDIR)/%.owl: + @echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))." +endif @@ -562,9 +622,13 @@ ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $< # ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base" ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) -# base: All the axioms as they are editted by the editors, excluding reasoning -$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) - $(ROBOT_RELEASE_IMPORT_MODE_BASE) \ +# base: A version of the ontology that does not include any externally imported axioms. +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \ + relax \ + reduce -r ELK \ + remove --base-iri http://purl.obolibrary.org/obo/PATO_ --base-iri http://purl.obolibrary.org/obo/pato# --axioms external --preserve-structure false --trim false \ $(SHARED_ROBOT_COMMANDS) \ annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ @@ -581,7 +645,7 @@ $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) # remove --select imports --trim false $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES) $(ROBOT_RELEASE_IMPORT_MODE) \ - reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \ relax \ remove --axioms equivalent \ relax \ @@ -648,13 +712,16 @@ update_repo: update_docs: mkdocs gh-deploy --config-file ../../mkdocs.yaml -# Note to future generations: prepending ./ is a safety measure to ensure that -# the environment does not malicously set `CLEANFILES` to `\`. +# Note to future generations: computing the real path relative to the +# current directory is a way to ensure we only clean up directories that +# are located below the current directory, regardless of the contents of +# the *DIR variables. .PHONY: clean clean: - [ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/* - [ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/* - [ -n "$(UPDATEREPODIR)" ] && [ $(UPDATEREPODIR) != "." ] && [ $(UPDATEREPODIR) != "/" ] && [ $(UPDATEREPODIR) != ".." ] && [ -d ./$(UPDATEREPODIR) ] && rm -rf ./$(UPDATEREPODIR)/* + for dir in $(MIRRORDIR) $(TMPDIR) $(UPDATEREPODIR) ; do \ + reldir=$$(realpath --relative-to=$$(pwd) $$dir) ; \ + case $$reldir in .*|"") ;; *) rm -rf $$reldir/* ;; esac \ + done rm -f $(CLEANFILES) .PHONY: help @@ -673,6 +740,7 @@ Core commands: * prepare_release_fast: Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns. * update_repo: Update the ODK repository setup using the config file pato-odk.yaml * test: Running all validation tests +* test_fast: Runs the test suite, but without updating imports or components * odkversion: Show the current version of the ODK Makefile and ROBOT. * clean: Delete all temporary files * help: Print ODK Usage information @@ -690,8 +758,8 @@ Imports management: Editor utilities: * validate_idranges: Make sure your ID ranges file is formatted correctly -* normalize_src: Load and safe your pato-edit file after you to make sure its serialised correctly -* normalize_obo_src: Load and safe your pato-edit.obo file after you to merge duplicate annotation assertions +* normalize_src: Load and save your pato-edit file after you to make sure its serialised correctly +* normalize_obo_src: Load and save your pato-edit.obo file after you to merge duplicate annotation assertions * explain_unsat: If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes * validate-all-tsv: Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files * validate-tsv: Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv. diff --git a/src/ontology/run.sh b/src/ontology/run.sh index cebc839..833f7e6 100755 --- a/src/ontology/run.sh +++ b/src/ontology/run.sh @@ -14,6 +14,8 @@ # # See README-editors.md for more details. +set -e + if [ -f run.sh.conf ]; then . ./run.sh.conf fi @@ -29,6 +31,22 @@ elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/tok GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token") fi +# SSH agent socket +# On macOS, we cannot use $SSH_AUTH_SOCK directly, +# we need to use a "magic" socket instead. +case "$(uname)" in +Darwin) + ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock + ;; +*) + ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK + ;; +esac +ODK_SSH_BIND= +if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then + ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock" +fi + ODK_IMAGE=${ODK_IMAGE:-odkfull} TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }') if [ -n "$TAG_IN_IMAGE" ]; then @@ -40,16 +58,28 @@ ODK_TAG=${ODK_TAG:-latest} ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx12G} ODK_DEBUG=${ODK_DEBUG:-no} +ODK_USER_ID=${ODK_USER_ID:-$(id -u)} +ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)} + +# Convert OWLAPI_* environment variables to the OWLAPI as Java options +# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html +# for a list of allowed options +OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions +for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do + ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}" +done + TIMECMD= if [ x$ODK_DEBUG = xyes ]; then # If you wish to change the format string, take care of using # non-breaking spaces (U+00A0) instead of normal spaces, to # prevent the shell from tokenizing the format string. - echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps." + echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps." TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb" fi +rm -f tmp/debug.log -VOLUME_BIND=$PWD/../../:/work +VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND WORK_DIR=/work/src/ontology if [ -n "$ODK_BINDS" ]; then @@ -59,14 +89,14 @@ fi if [ -n "$USE_SINGULARITY" ]; then singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \ - --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \ + --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \ --bind $VOLUME_BIND \ -W $WORK_DIR \ docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" else BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')" docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \ - -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \ + -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \ --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" fi diff --git a/src/scripts/run-command.sh b/src/scripts/run-command.sh new file mode 100755 index 0000000..45d431d --- /dev/null +++ b/src/scripts/run-command.sh @@ -0,0 +1,4 @@ +#!/bin/sh +ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log} +echo "Command: sh $@" >> $ODK_DEBUG_FILE +/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@" diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh index 4227840..085abe4 100644 --- a/src/scripts/update_repo.sh +++ b/src/scripts/update_repo.sh @@ -26,7 +26,8 @@ cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/ cp -r target/$OID/src/sparql/* $SRCDIR/sparql/ mkdir -p $ROOTDIR/.github mkdir -p $ROOTDIR/.github/workflows -cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml +cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml + cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml @@ -35,5 +36,5 @@ cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml cp -n target/$OID/mkdocs.yaml $ROOTDIR/ echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)" -echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml." + echo "Ontology repository update successfully completed." \ No newline at end of file diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql index 0c4d284..a6a4851 100644 --- a/src/sparql/class-count-by-prefix.sparql +++ b/src/sparql/class-count-by-prefix.sparql @@ -7,4 +7,4 @@ SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE FILTER (!isBlank(?cls)) BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) } -GROUP BY ?prefix +GROUP BY ?prefix \ No newline at end of file