diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl index e2826e88..f7b231af 100644 --- a/src/ontology/imports/chebi_import.owl +++ b/src/ontology/imports/chebi_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-04-01") + +Annotation( ) +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) Declaration(Class()) @@ -252,6 +252,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1153,6 +1154,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1186,6 +1188,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1253,7 +1256,12 @@ 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()) @@ -1797,8 +1805,8 @@ AnnotationAssertion(Annotation( "CHEBI:132988") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bradykinin(2+)") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (saturated dicarboxylic acid dianion(2-)) @@ -6780,7 +6788,7 @@ SubClassOf( ObjectSomeValuesFrom( "A compound RC(=O)H, in which a carbonyl group is bonded to one hydrogen atom and to one R group.") AnnotationAssertion( "0") AnnotationAssertion( "CHOR") -AnnotationAssertion( "29.01800") +AnnotationAssertion( "29.018") AnnotationAssertion( "29.00274") AnnotationAssertion( "[H]C([*])=O") AnnotationAssertion( "CHEBI:13432") @@ -9278,6 +9286,17 @@ AnnotationAssertion(rdfs:label "bra SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (fatty amide anion) + +AnnotationAssertion( "The conjugate base of a fatty amide, arising from deprotonation of the carboxylic acid group of the corresponding fatty amide.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "fatty amide anions") +AnnotationAssertion( "CHEBI:229684") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "fatty amide anion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (calcium atom) AnnotationAssertion( "0") @@ -12990,11 +13009,8 @@ SubClassOf( ObjectSomeValuesFrom( "A racemate comprising equimolar amounts of (R)- and (S)-lactic acid.") AnnotationAssertion( "0") AnnotationAssertion( "C3H6O3") -AnnotationAssertion( "InChI=1S/2C3H6O3/c2*1-2(4)3(5)6/h2*2,4H,1H3,(H,5,6)/t2*2-/m10/s1") -AnnotationAssertion( "KVZLHPXEUGJPAH-QNDGGIRCSA-N") -AnnotationAssertion( "180.156") -AnnotationAssertion( "180.06339") -AnnotationAssertion( "C(=O)([C@@H](O)C)O.C(=O)([C@H](O)C)O") +AnnotationAssertion( "90.07794") +AnnotationAssertion( "90.03169") AnnotationAssertion( "CHEBI:24998") AnnotationAssertion( "CHEBI:6351") AnnotationAssertion(Annotation( "Beilstein") "Beilstein:1209341") @@ -13897,6 +13913,7 @@ AnnotationAssertion(rdfs:label "fat SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (methanediide) @@ -14148,7 +14165,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "L-glutamate(1-)") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -15428,7 +15444,7 @@ AnnotationAssertion(rdfs:label "brad SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (arachidonate) @@ -16803,7 +16819,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic group") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (hydrocarbyl group) @@ -17765,7 +17782,7 @@ SubClassOf( "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") @@ -18163,7 +18180,9 @@ AnnotationAssertion(Annotation( "CHEBI:33703") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino-acid cation") +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (alpha-amino acid) @@ -18191,6 +18210,7 @@ AnnotationAssertion( "alpha-amino acid") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (beta-amino acid) @@ -18227,6 +18247,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino-acid residue") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (amino acid) @@ -18246,6 +18268,7 @@ AnnotationAssertion(rdfs:label "ami SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (alpha-amino-acid residue) @@ -18274,6 +18297,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "alpha-amino-acid cation") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (carbohydrate acid) @@ -24584,8 +24608,8 @@ AnnotationAssertion( "CC1=C(C=C)\\C(NC1=O)=C\\c1[nH]c(Cc2[nH]c(\\C=C3NC(=O)C(C=C)=C/3C)c(C)c2CCC([O-])=O)c(CCC([O-])=O)c1C") AnnotationAssertion(Annotation( "Beilstein") "Beilstein:4083310") AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "UniProt") "(4Z,15Z)-bilirubin IXalpha") AnnotationAssertion(Annotation( "ChEBI") "2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoate") -AnnotationAssertion(Annotation( "UniProt") "bilirubin IXalpha") AnnotationAssertion(Annotation( "ChEBI") "bilirubin dianion") AnnotationAssertion( "CHEBI:57977") AnnotationAssertion( ) @@ -24791,6 +24815,23 @@ AnnotationAssertion(rdfs:label "N-a SubClassOf( ) 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: (organophosphate oxoanion) AnnotationAssertion( "An organic phosphoric acid derivative in which one or more oxygen atoms of the phosphate group(s) has been deprotonated.") @@ -25295,6 +25336,16 @@ AnnotationAssertion(rdfs:label "ion SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (peptide cation) + +AnnotationAssertion( "A cation formed by protonation of a peptide.") +AnnotationAssertion( "chebi_ontology") +AnnotationAssertion(Annotation( "ChEBI") "peptide cations") +AnnotationAssertion( "CHEBI:60194") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "peptide cation") +SubClassOf( ) + # Class: (monovalent inorganic cation) AnnotationAssertion( "An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.") @@ -26279,6 +26330,48 @@ 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: (cosmetic) AnnotationAssertion( "The role played by a substance in enhancing the appearance or odour of the human body; a name given to the substance itself or to a component of it.") @@ -26291,6 +26384,23 @@ AnnotationAssertion( "cosmetic") SubClassOf( ) +# 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.") diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl index 174f6319..3bee1fd4 100644 --- a/src/ontology/imports/cl_import.owl +++ b/src/ontology/imports/cl_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-04-01") + +Annotation( ) +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) Declaration(Class()) @@ -694,6 +694,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -706,14 +707,8 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -721,13 +716,10 @@ 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()) @@ -751,8 +743,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -768,7 +758,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -784,8 +773,6 @@ Declaration(AnnotationProperty()) # Annotation Property: (definition) -AnnotationAssertion( "definition"@en) -AnnotationAssertion( ) AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) AnnotationAssertion( "2012-04-05: Barry Smith @@ -807,21 +794,15 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") # Annotation Property: (has ontology root term) -AnnotationAssertion( "has ontology root term"@en) AnnotationAssertion( "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root."@en) -AnnotationAssertion( "Nicolas Matentzoglu"@en) AnnotationAssertion( "IAO:0000700") AnnotationAssertion( "external") -AnnotationAssertion( "uberon") AnnotationAssertion( "has_ontology_root_term") -AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "has_ontology_root_term") AnnotationAssertion(rdfs:label "has ontology root term"@en) @@ -830,11 +811,7 @@ AnnotationAssertion(rdfs:label "pre # Annotation Property: (term replaced by) -AnnotationAssertion( "term replaced by"@en) -AnnotationAssertion( ) AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) AnnotationAssertion(rdfs:label "term replaced by"@en) AnnotationAssertion(rdfs:label "term replaced by") @@ -907,60 +884,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (creator) - -AnnotationAssertion( "http://purl.org/dc/elements/1.1/creator") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-creator") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-creator") -AnnotationAssertion(rdfs:label "creator") - -# Annotation Property: (description) - -AnnotationAssertion( "http://purl.org/dc/elements/1.1/description") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-description") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-description") -AnnotationAssertion(rdfs:label "description") - -# Annotation Property: (title) - -AnnotationAssertion( "http://purl.org/dc/elements/1.1/title") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-title") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-title") -AnnotationAssertion(rdfs:label "title") - -# Annotation Property: (contributor) - -AnnotationAssertion( "http://purl.org/dc/terms/contributor") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dc-contributor") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dc-contributor") -AnnotationAssertion(rdfs:label "contributor") - -# Annotation Property: (date) - -AnnotationAssertion( "http://purl.org/dc/terms/date") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dcterms-date") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dcterms-date") -AnnotationAssertion(rdfs:label "date") - -# Annotation Property: (license) - -AnnotationAssertion( "http://purl.org/dc/terms/license") -AnnotationAssertion( "uberon") -AnnotationAssertion( "dcterms-license") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "dcterms-license") -AnnotationAssertion(rdfs:label "license") - # Annotation Property: (subset_property) AnnotationAssertion(rdfs:label "subset_property") @@ -984,7 +907,6 @@ AnnotationAssertion(rdfs:label (has_broad_synonym) AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") -AnnotationAssertion( ) AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") AnnotationAssertion(rdfs:label "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") @@ -997,7 +919,6 @@ AnnotationAssertion(rdfs:label (has exact synonym) AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") -AnnotationAssertion( ) AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") AnnotationAssertion(rdfs:label "has exact synonym"@en) AnnotationAssertion(rdfs:label "has_exact_synonym") @@ -1006,7 +927,6 @@ AnnotationAssertion(rdfs:seeAlso (has narrow synonym) AnnotationAssertion( "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") -AnnotationAssertion( ) AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") AnnotationAssertion(rdfs:label "has narrow synonym"@en) AnnotationAssertion(rdfs:label "has_narrow_synonym") @@ -1019,7 +939,6 @@ AnnotationAssertion(rdfs:label (has_related_synonym) AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") -AnnotationAssertion( ) AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") AnnotationAssertion(rdfs:label "has related synonym"@en) AnnotationAssertion(rdfs:label "has_related_synonym") @@ -1038,31 +957,17 @@ AnnotationAssertion(rdfs:label (part_of) +# Object Property: (part of) -AnnotationAssertion( "is part of"@en) -AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) -AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) AnnotationAssertion( "a core relation that holds between a part and its whole"@en) AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) -AnnotationAssertion( "part_of"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "BFO:0000050") AnnotationAssertion( "external") AnnotationAssertion( "quality") -AnnotationAssertion( "uberon") AnnotationAssertion( "part_of") AnnotationAssertion( ) AnnotationAssertion( ) @@ -1081,22 +986,15 @@ TransitiveObjectProperty() # Object Property: (has part) -AnnotationAssertion( "has part"@en) -AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) -AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) AnnotationAssertion( "a core relation that holds between a whole and its part"@en) AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) -AnnotationAssertion( "has_part"@en) -AnnotationAssertion( ) AnnotationAssertion( "BFO:0000051") AnnotationAssertion( "external") AnnotationAssertion( "quality") -AnnotationAssertion( "uberon") AnnotationAssertion( "has_part") AnnotationAssertion( ) AnnotationAssertion( ) @@ -1109,53 +1007,27 @@ TransitiveObjectProperty() # Object Property: (located in) -AnnotationAssertion( "located in"@en) -AnnotationAssertion( "my brain is located in my head"@en) -AnnotationAssertion( "this rat is located in this cage"@en) AnnotationAssertion( "a relation between two independent continuants, the target and the location, in which the target is entirely within the location"@en) AnnotationAssertion( "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus"@en) AnnotationAssertion( "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "located_in"@en) -AnnotationAssertion( ) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:located_in") -AnnotationAssertion( "RO:0001025") -AnnotationAssertion( "uberon") -AnnotationAssertion( "located_in") AnnotationAssertion( ) -AnnotationAssertion( "located_in") AnnotationAssertion(rdfs:label "located in"@en) -AnnotationAssertion(rdfs:label "located in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Located_in"^^xsd:anyURI) TransitiveObjectProperty() # Object Property: (synapsed by) -AnnotationAssertion( ) AnnotationAssertion( "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. "@en) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( " some ( that part_of some ( that has_part some ( that some Y?)))") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002103") -AnnotationAssertion( "uberon") -AnnotationAssertion( "synapsed_by") -AnnotationAssertion( "synapsed_by") AnnotationAssertion(rdfs:label "synapsed by"@en) -AnnotationAssertion(rdfs:label "synapsed by") InverseObjectProperties( ) ObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( ))) # Object Property: (synapsed to) -AnnotationAssertion( ) AnnotationAssertion( " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. "@en) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( " some ( that part_of some ( that some ( that some Y?)))") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -1168,83 +1040,42 @@ ObjectPropertyDomain( ObjectUnionOf(< # Object Property: (develops from) -AnnotationAssertion( ) AnnotationAssertion( "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002202") -AnnotationAssertion( "uberon") -AnnotationAssertion( "develops_from") -AnnotationAssertion( "develops_from") AnnotationAssertion(rdfs:comment "This is the transitive form of the develops from relation") AnnotationAssertion(rdfs:label "develops from"@en) -AnnotationAssertion(rdfs:label "develops from") InverseObjectProperties( ) TransitiveObjectProperty() # Object Property: (develops into) -AnnotationAssertion( ) AnnotationAssertion( "inverse of develops from") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002203") -AnnotationAssertion( "uberon") -AnnotationAssertion( "develops_into") AnnotationAssertion( ) -AnnotationAssertion( "develops_into") AnnotationAssertion(rdfs:label "develops into"@en) -AnnotationAssertion(rdfs:label "develops into") SubObjectPropertyOf( ) TransitiveObjectProperty() # Object Property: (directly develops from) -AnnotationAssertion( ) AnnotationAssertion( "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "FBbt") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002207") AnnotationAssertion( "has developmental precursor") -AnnotationAssertion( "uberon") -AnnotationAssertion( "directly_develops_from") -AnnotationAssertion( "directly_develops_from") AnnotationAssertion(rdfs:comment "TODO - add child relations from DOS") AnnotationAssertion(rdfs:label "directly develops from"@en) -AnnotationAssertion(rdfs:label "directly develops from") SubObjectPropertyOf( ) # Object Property: (has potential to directly develop into) -AnnotationAssertion( ) AnnotationAssertion( "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y"@en) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has potential to directly develop into"@en) # Object Property: (existence starts during) AnnotationAssertion( "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002488") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_starts_during") -AnnotationAssertion( "existence_starts_during") AnnotationAssertion(rdfs:label "existence starts during") # Object Property: (existence starts and ends during) AnnotationAssertion( "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002491") AnnotationAssertion( "exists during") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_starts_and_ends_during") -AnnotationAssertion( "existence_starts_and_ends_during") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence starts and ends during") SubObjectPropertyOf( ) @@ -1252,14 +1083,7 @@ SubObjectPropertyOf( (existence ends during) -AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.") AnnotationAssertion( "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002492") -AnnotationAssertion( "ceases_to_exist_during") -AnnotationAssertion( "uberon") -AnnotationAssertion( "existence_ends_during") -AnnotationAssertion( "existence_ends_during") AnnotationAssertion(rdfs:comment "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label "existence ends during") @@ -5659,11 +5483,11 @@ SubClassOf( (perivascular macrophage) -AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "GO_REF:0000031") Annotation( "PMID:16507898") "A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+.") -AnnotationAssertion(rdfs:comment "Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+.") +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "GO_REF:0000031") Annotation( "PMID:16507898") Annotation( "PMID:37232741") "A border associated macrophage that is adjacent to a small blood vessel of a brain. A perivascular macrophage expresses the markers CD14, CD16 and CD163. In homeostatic conditions, this central nervous system macrophage has a non-motile cell body with extending and retracting projections through the blood vessel wall.") +AnnotationAssertion(Annotation( "PMID:37232741") Annotation( ) "pvMΦ") AnnotationAssertion(rdfs:label "perivascular macrophage") -SubClassOf(Annotation( "true") ) SubClassOf( ) +SubClassOf(Annotation( "true") ) # Class: (foam cell) @@ -8165,6 +7989,7 @@ SubClassOf( "camera type eye photoreceptor cell") AnnotationAssertion(rdfs:label "camera-type eye photoreceptor cell") SubClassOf( ) +SubClassOf( ) # Class: (cerebral cortex neuron) @@ -9006,6 +8831,18 @@ AnnotationAssertion( "fetal pre-type II pneumocyte") SubClassOf( ) +# Class: (border associated macrophage) + +AnnotationAssertion(Annotation( "PMID:37232741") Annotation( "PMID:37626977") "A central nervous system macrophage that is part of a choroid plexus, a meninx and a perivascular space. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-03-26T16:39:56Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "PMID:36945367") Annotation( ) "BAM") +AnnotationAssertion(Annotation( "PMID:33556248") Annotation( ) "CAM") +AnnotationAssertion(Annotation( "PMID:37232741") "CNS-associated macrophage") +AnnotationAssertion(Annotation( "PMID:29426702") Annotation( "PMID:37232741") rdfs:comment "In humans, a border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169.") +AnnotationAssertion(rdfs:label "border associated macrophage"@en) +SubClassOf( ) + SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index 972ba2e6..40133d65 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -7,12 +7,11 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-04-01") + +Annotation( ) +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -619,8 +618,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -900,6 +897,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1007,8 +1006,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1535,7 +1532,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1565,7 +1561,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1627,7 +1622,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1973,7 +1967,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2039,7 +2032,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2068,7 +2060,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2076,7 +2067,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2108,6 +2098,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3204,7 +3195,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3588,9 +3578,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3622,6 +3609,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4104,8 +4092,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4357,20 +4343,23 @@ 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()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -4428,10 +4417,6 @@ AnnotationAssertion(rdfs:label "ter SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -4448,6 +4433,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -4472,6 +4461,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -4480,6 +4473,10 @@ SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) @@ -4613,24 +4610,6 @@ AnnotationAssertion( "mitochondrial genome maintenance") SubClassOf( ) -# 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( ) -DisjointClasses( ) - # Class: (single strand break repair) AnnotationAssertion(Annotation( "PMID:18626472") "The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.") @@ -4964,7 +4943,7 @@ AnnotationAssertion( "GOC:dph") Annotation( "GOC:tb") "cytokinesis involved in cell cycle") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0000910") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -5114,7 +5093,7 @@ 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( ) @@ -5126,7 +5105,6 @@ AnnotationAssertion( "follicular phase") AnnotationAssertion( "GO:0001541") AnnotationAssertion(rdfs:label "ovarian follicle development") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -5782,6 +5760,8 @@ SubClassOf( (regulation of cytokine production) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") "Any process that modulates the frequency, rate, or extent of production of a cytokine.") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "GO:0042035") AnnotationAssertion( "GO:0050707") AnnotationAssertion( "regulation of cytokine anabolism") @@ -9567,7 +9547,7 @@ SubClassOf( ObjectSomeValuesFrom( "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( ))) @@ -9583,7 +9563,7 @@ 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( ))) @@ -9601,7 +9581,7 @@ 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( ))) @@ -10262,7 +10242,7 @@ 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( ) @@ -10943,11 +10923,14 @@ AnnotationAssertion( "GO:0003824") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "catalytic activity") SubClassOf( ) @@ -11146,7 +11129,7 @@ AnnotationAssertion( "RHEA:17825") AnnotationAssertion(Annotation(rdfs:label "Defective HK1 does not phosphorylate Glc to form G6P") "Reactome:R-HSA-5621888") AnnotationAssertion(Annotation(rdfs:label "Defective GCK does not phosphorylate Glc to form G6P") "Reactome:R-HSA-5621918") -AnnotationAssertion(Annotation(rdfs:label "HK1,2,3,GCK phosphorylate Glc to form G6P") "Reactome:R-HSA-70420") +AnnotationAssertion(Annotation(rdfs:label "HK1,2,3,GCK,HKDC1 phosphorylate Glc to form G6P") "Reactome:R-HSA-70420") AnnotationAssertion( "molecular_function") AnnotationAssertion(Annotation( "EC:2.7.1.2") "ATP:D-glucose 6-phosphotransferase activity") AnnotationAssertion(Annotation( "EC:2.7.1.2") "glucokinase (phosphorylating)") @@ -11313,7 +11296,7 @@ AnnotationAssertion(Annotation(rdfs:label "CYP4F22 20-hydroxylates TrXA3") "Reactome:R-HSA-5605147") AnnotationAssertion(Annotation(rdfs:label "Tyrosinase oxidises tyrosine to dopaquinone") "Reactome:R-HSA-5662662") AnnotationAssertion(Annotation(rdfs:label "Dopa is oxidized to dopaquinone by TYR") "Reactome:R-HSA-5662692") -AnnotationAssertion(Annotation(rdfs:label "DHI and DHICA polymerise forming eumelanin") "Reactome:R-HSA-5663050") +AnnotationAssertion(Annotation(rdfs:label "DHI and DHICA polymerize forming eumelanin") "Reactome:R-HSA-5663050") AnnotationAssertion(Annotation(rdfs:label "CYP4V2 omega-hydroxylates DHA to HDoHE") "Reactome:R-HSA-6786239") AnnotationAssertion(Annotation(rdfs:label "Vinyl chloride is oxidized to 2-Chloroethylene oxide") "Reactome:R-HSA-76354") AnnotationAssertion(Annotation(rdfs:label "N-hydroxylation of 4-aminobiphenyl") "Reactome:R-HSA-76373") @@ -11699,8 +11682,6 @@ SubClassOf( "GOC:ai") Annotation( "GOC:dgf") "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.") AnnotationAssertion( "GO:0005478") -AnnotationAssertion(Annotation(rdfs:label "Virion-associated M2 protein mediated ion infusion") "Reactome:R-HSA-168313") -AnnotationAssertion(Annotation(rdfs:label "SMAD7:SMURF1 complex is exported to the cytosol") "Reactome:R-HSA-178215") AnnotationAssertion( "molecular_function") AnnotationAssertion( "carrier") AnnotationAssertion( "GO:0005215") @@ -11708,13 +11689,16 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.") AnnotationAssertion(rdfs:label "transporter activity") SubClassOf( ) @@ -11760,6 +11744,7 @@ AnnotationAssertion(Annotation(rdfs:label "Decreasing cGMP concentration promote AnnotationAssertion(Annotation(rdfs:label "SARS-CoV-1 E transports Ca2+") "Reactome:R-HSA-9706720") AnnotationAssertion(Annotation(rdfs:label "cAMP:olfactory CNG channel translocates Na+ and Ca2+ from the extracellular region to the cytosol") "Reactome:R-HSA-9712190") AnnotationAssertion(Annotation(rdfs:label "SARS-CoV-2 E pentamer transports Ca2+") "Reactome:R-HSA-9754616") +AnnotationAssertion(Annotation(rdfs:label "SH pentamer transports K+") "Reactome:R-HSA-9837835") AnnotationAssertion( "cation diffusion facilitator activity") AnnotationAssertion( "non-selective cation channel activity") AnnotationAssertion( "molecular_function") @@ -11843,9 +11828,12 @@ AnnotationAssertion( "GO:0005515") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein binding") SubClassOf( ) @@ -11879,13 +11867,16 @@ 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") @@ -11966,7 +11957,6 @@ 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( ) @@ -12004,12 +11994,14 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleus") SubClassOf( ) @@ -12072,6 +12064,7 @@ 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") @@ -12107,7 +12100,9 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cytoplasm") SubClassOf( ) @@ -12125,11 +12120,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)") AnnotationAssertion(rdfs:label "mitochondrion") @@ -12211,11 +12208,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vacuole") SubClassOf( ) @@ -12244,8 +12243,10 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peroxisome") SubClassOf( ) @@ -12262,10 +12263,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endoplasmic reticulum") SubClassOf( ) @@ -12301,10 +12304,12 @@ 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") @@ -12375,6 +12380,7 @@ AnnotationAssertion( "GO:0005815") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "microtubule organizing center") @@ -12404,11 +12410,14 @@ AnnotationAssertion( "GO:0005840") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ribosome") SubClassOf( ) @@ -12423,11 +12432,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cytoskeleton") @@ -12548,11 +12559,14 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "plasma membrane") SubClassOf( ) @@ -12696,6 +12710,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -12731,7 +12746,10 @@ SubClassOf( (glycogen catabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27107"^^xsd:anyURI) AnnotationAssertion( "MetaCyc:GLYCOCAT-PWY") +AnnotationAssertion( "MetaCyc:PWY-5941") +AnnotationAssertion( "MetaCyc:PWY-7662") AnnotationAssertion( "glycogen breakdown") AnnotationAssertion( "glycogen catabolism") AnnotationAssertion( "glycogen degradation") @@ -12835,12 +12853,15 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "generation of precursor metabolites and energy") SubClassOf( ) @@ -13054,6 +13075,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "DNA metabolic process") SubClassOf( ) @@ -13066,6 +13089,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006260") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -13139,6 +13163,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006281") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -13193,37 +13218,18 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "double-strand break repair") SubClassOf( ) -# Class: (DNA modification) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:ma") "The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006304") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "DNA modification") -SubClassOf( ) -SubClassOf( ) +# Class: (obsolete DNA methylation) -# Class: (DNA alkylation) - -AnnotationAssertion(Annotation( "ISBN:0716735970") "The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006305") -AnnotationAssertion(rdfs:label "DNA alkylation") -SubClassOf( ) - -# Class: (DNA methylation) - -AnnotationAssertion(Annotation( "GOC:ems") Annotation( "ISBN:0198506732") "The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) +AnnotationAssertion(Annotation( "GOC:ems") Annotation( "ISBN:0198506732") "OBSOLETE. The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.") +AnnotationAssertion( "GO:0009008") +AnnotationAssertion( "GO:0009307") +AnnotationAssertion( "GO:0031507") AnnotationAssertion( "Wikipedia:DNA_methylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006306") -AnnotationAssertion(rdfs:label "DNA methylation") -SubClassOf( ) -SubClassOf( ) +AnnotationAssertion(rdfs:comment "This term was obsoleted because it represents a molecular function.") +AnnotationAssertion(rdfs:label "obsolete DNA methylation") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Class: (DNA recombination) @@ -13231,6 +13237,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0006310") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -13321,12 +13328,14 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006351") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "DNA-templated transcription") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -13348,6 +13357,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of DNA-templated transcription") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -13385,14 +13395,16 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "translation") SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -13424,7 +13436,6 @@ AnnotationAssertion( "regulation of translation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -13446,8 +13457,7 @@ AnnotationAssertion( "GO:0006518") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "peptide metabolic process") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (amino acid metabolic process) @@ -13466,6 +13476,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino acid metabolic process") SubClassOf( ) @@ -13516,13 +13527,16 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lipid metabolic process") SubClassOf( ) @@ -13701,7 +13715,7 @@ SubClassOf( (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(Annotation( "GOC:ai") "The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus.") AnnotationAssertion( "phosphorus metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006793") @@ -13768,7 +13782,9 @@ 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( ) @@ -13911,8 +13927,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino acid transport") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (lipid transport) @@ -14088,6 +14103,7 @@ AnnotationAssertion( "GO:0006914") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -14239,12 +14255,12 @@ 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( ) @@ -14398,6 +14414,7 @@ AnnotationAssertion( "mitochondrion biogenesis") AnnotationAssertion(Annotation( "GOC:mah") "mitochondrion organisation") AnnotationAssertion( "biological_process") +AnnotationAssertion( "mitochondrion morphogenesis") AnnotationAssertion( "mitochondrion organization and biogenesis") AnnotationAssertion( "GO:0007005") AnnotationAssertion( ) @@ -14517,13 +14534,14 @@ 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( ) @@ -14550,7 +14568,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0007060") AnnotationAssertion(rdfs:label "male meiosis chromosome segregation") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -14648,7 +14665,6 @@ AnnotationAssertion( "GO:0007112") AnnotationAssertion(rdfs:label "male meiosis cytokinesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -14662,7 +14678,6 @@ AnnotationAssertion( "GO:0007140") AnnotationAssertion(rdfs:label "male meiotic nuclear division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -14677,7 +14692,6 @@ AnnotationAssertion( "Note that female germ lines can be found in female or hermaphroditic organisms, so this term can be used to annotate gene products from hermaphrodites such as those of C. elegans. See also the biological process term 'meiotic nuclear division; GO:0140013'.") AnnotationAssertion(rdfs:label "female meiotic nuclear division") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -14706,6 +14720,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -14749,20 +14764,17 @@ 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( ) @@ -14773,7 +14785,8 @@ SubClassOf( ObjectSomeValuesFrom( (cell surface receptor signaling pathway) -AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:mah") Annotation( "GOC:pr") Annotation( "GOC:signaling") "The series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.") +AnnotationAssertion(Annotation( "GOC:signaling") "The series of molecular signals initiated by an extracellular ligand binding to a receptor located on the cell surface. The pathway ends with regulation of a downstream cellular process, e.g. transcription.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26960") AnnotationAssertion( "cell surface receptor linked signal transduction") AnnotationAssertion(Annotation( "GOC:bf") "cell surface receptor linked signaling pathway") AnnotationAssertion(Annotation( "GOC:mah") "cell surface receptor linked signalling pathway") @@ -14994,7 +15007,6 @@ AnnotationAssertion( "GO:0007343") AnnotationAssertion(rdfs:label "egg activation") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of mitotic cell cycle) @@ -15209,6 +15221,7 @@ SubClassOf( (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") @@ -15480,7 +15493,7 @@ 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. @@ -15548,6 +15561,7 @@ AnnotationAssertion( "GO:0007623") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "circadian rhythm") SubClassOf( ) @@ -15756,6 +15770,7 @@ AnnotationAssertion(rdfs:label "biol # Class: (metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198547684") "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-17T15:46:40Z") AnnotationAssertion( "GO:0044236") @@ -15768,11 +15783,13 @@ 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( ) @@ -15965,12 +15982,12 @@ SubClassOf( ObjectSomeValuesFrom( "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") AnnotationAssertion(rdfs:label "germ cell migration") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (asymmetric cell division) @@ -16120,8 +16137,10 @@ SubClassOf( (P-type potassium transmembrane transporter activity) AnnotationAssertion(Annotation( "RHEA:16777") "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + K+(out) = ADP + phosphate + K+(in).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26941"^^xsd:anyURI) AnnotationAssertion( "GO:0015618") AnnotationAssertion( "EC:7.2.2.6") +AnnotationAssertion( "MetaCyc:TRANS-RXN-2") AnnotationAssertion( "RHEA:16777") AnnotationAssertion( "ATP-dependent potassium transmembrane transporter activity") AnnotationAssertion( "K+-transporting ATPase activity") @@ -16269,6 +16288,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "catabolic process") SubClassOf( ) @@ -16311,6 +16331,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "biosynthetic process") SubClassOf( ) @@ -16799,7 +16820,7 @@ 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.") @@ -16812,7 +16833,7 @@ 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.") @@ -16866,7 +16887,7 @@ 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.") @@ -16908,6 +16929,29 @@ AnnotationAssertion(rdfs:label "anat SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (response to endogenous stimulus) + +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(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") +SubClassOf( ) + +# Class: (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(Annotation( "GOC:dos") "response to hormone stimulus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "growth regulator") +AnnotationAssertion( "GO:0009725") +AnnotationAssertion(rdfs:label "response to hormone") +SubClassOf( ) +SubClassOf( ) + # Class: (regulation of asymmetric cell division) AnnotationAssertion(Annotation( "GOC:lr") "Any process that modulates the frequency, rate or extent of asymmetric cell division.") @@ -16928,7 +16972,7 @@ AnnotationAssertion( "embryonal development") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009790") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "embryo development") @@ -17506,6 +17550,8 @@ 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( ))) @@ -18064,7 +18110,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -18189,30 +18234,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (positive regulation of mitochondrion organization) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion.") -AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of mitochondrion organisation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010822") -AnnotationAssertion(rdfs:label "positive regulation of mitochondrion organization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of mitochondrion organization) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion.") -AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of mitochondrion organisation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010823") -AnnotationAssertion(rdfs:label "negative regulation of mitochondrion organization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of glucose transmembrane transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") @@ -18402,7 +18423,7 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of phosphatase activity) -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.") +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing phosphate.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010921") AnnotationAssertion( ) @@ -18691,9 +18712,11 @@ 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") @@ -18893,6 +18916,7 @@ AnnotationAssertion(rdfs:label "glut SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (regulation of glutamate secretion) @@ -18901,6 +18925,7 @@ AnnotationAssertion( "GO:0014048") AnnotationAssertion(rdfs:label "regulation of glutamate secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -18918,6 +18943,7 @@ AnnotationAssertion( "positive regulation of glutamate secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -18934,6 +18960,7 @@ AnnotationAssertion( "negative regulation of glutamate secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -19004,7 +19031,7 @@ AnnotationAssertion( "GO:0014060") AnnotationAssertion(rdfs:label "regulation of epinephrine secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of norepinephrine secretion) @@ -19309,6 +19336,7 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:ai") "Enables the transfer of a proton from one side of a membrane to the other.") AnnotationAssertion(Annotation(rdfs:label "Intraphagosomal pH is lowered to 5 by V-ATPase") "Reactome:R-HSA-1222516") AnnotationAssertion(Annotation(rdfs:label "Enzyme-bound ATP is released") "Reactome:R-HSA-164834") +AnnotationAssertion(Annotation(rdfs:label "Virion-associated M2 protein mediated ion infusion") "Reactome:R-HSA-168313") AnnotationAssertion(Annotation(rdfs:label "Protons are translocated from the intermembrane space to the matrix") "Reactome:R-HSA-170026") AnnotationAssertion(Annotation(rdfs:label "Endosome acidification") "Reactome:R-HSA-74723") AnnotationAssertion(Annotation(rdfs:label "Acidification of Tf:TfR1 containing endosome") "Reactome:R-HSA-917841") @@ -19437,7 +19465,6 @@ AnnotationAssertion( "GO:0015404") AnnotationAssertion( "GO:0015570") AnnotationAssertion( "active transporter") -AnnotationAssertion(Annotation(rdfs:label "SLC25A16 transports cytosolic CoA-SH to mitichondrial matrix") "Reactome:R-HSA-199216") AnnotationAssertion( "TC:2.A") AnnotationAssertion( "coupled carrier") AnnotationAssertion( "electrochemical potential-driven transporter activity") @@ -19552,7 +19579,9 @@ SubClassOf( (sodium:proton antiporter activity) AnnotationAssertion(Annotation( "TC:2.A.35.1.1") Annotation( "TC:2.A.36.-.-") "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Na+(out) + H+(in) = Na+(in) + H+(out).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26941"^^xsd:anyURI) AnnotationAssertion( "GO:0015502") +AnnotationAssertion( "MetaCyc:TRANS-RXN-129") AnnotationAssertion( "RHEA:29251") AnnotationAssertion(Annotation(rdfs:label "SLC9B1/C2 exchange Na+ for H+") "Reactome:R-HSA-2872444") AnnotationAssertion(Annotation(rdfs:label "SLC9C1 exchanges Na+ for H+") "Reactome:R-HSA-2872463") @@ -19866,10 +19895,12 @@ 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") SubClassOf( ) @@ -19986,6 +20017,7 @@ AnnotationAssertion( "GO:0016070") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -20065,6 +20097,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -20078,6 +20111,9 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "EC:2.1.1.6") AnnotationAssertion( "MetaCyc:CATECHOL-O-METHYLTRANSFERASE-RXN") +AnnotationAssertion( "MetaCyc:RXN-10870") +AnnotationAssertion( "MetaCyc:RXN-9017") +AnnotationAssertion( "RHEA:17877") AnnotationAssertion(Annotation(rdfs:label "COMT transfer CH3 from AdoMet to 3,4DHBNZ") "Reactome:R-HSA-175983") AnnotationAssertion(Annotation(rdfs:label "LRTOMT transfers Met to DA, forming 3MT") "Reactome:R-HSA-8955010") AnnotationAssertion( "molecular_function") @@ -20098,10 +20134,13 @@ SubClassOf( "ISBN:0198506732") "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0016209") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "antioxidant activity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -20188,6 +20227,7 @@ 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") @@ -20196,9 +20236,11 @@ SubClassOf( (phosphorylation) AnnotationAssertion(Annotation( "ISBN:0198506732") "The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0016310") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phosphorylation") @@ -20207,9 +20249,11 @@ SubClassOf( (dephosphorylation) AnnotationAssertion(Annotation( "ISBN:0198506732") "The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Dephosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0016311") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "dephosphorylation") SubClassOf( ) @@ -20220,7 +20264,6 @@ AnnotationAssertion( "GO:0016321") AnnotationAssertion(rdfs:label "female meiosis chromosome segregation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20280,6 +20323,7 @@ SubClassOf( (somatic cell DNA recombination) AnnotationAssertion(Annotation( "GOC:ma") "Recombination occurring within or between DNA molecules in somatic cells.") +AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0016444") AnnotationAssertion(rdfs:label "somatic cell DNA recombination") @@ -20796,13 +20840,14 @@ SubClassOf( (phosphatase activity) -AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:pg") "Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.") +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:pg") "Catalysis of the hydrolysis of phosphoric monoesters, releasing phosphate ions.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25755"^^xsd:anyURI) AnnotationAssertion( "GO:0003869") AnnotationAssertion( "GO:0016302") AnnotationAssertion( "EC:3.1.3.-") AnnotationAssertion(Annotation(rdfs:label "Unknown pPPP phosphatase dephosphorylates pPPP to pPNOL") "Reactome:R-HSA-4419986") AnnotationAssertion(Annotation(rdfs:label "SapM dephosphorylates PI3P") "Reactome:R-HSA-9636457") +AnnotationAssertion(Annotation(rdfs:label "PANK4 hydrolyzes PPANT to pantetheine") "Reactome:R-HSA-9837419") AnnotationAssertion( "phosphoric monoester hydrolase activity") AnnotationAssertion( "molecular_function") AnnotationAssertion( "phosphatase") @@ -21088,7 +21133,6 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21185,10 +21229,9 @@ AnnotationAssertion( "single-organism reproductive behavior") AnnotationAssertion( "GO:0019098") AnnotationAssertion(rdfs:label "reproductive behavior") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( )) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (carbohydrate kinase activity) @@ -21413,6 +21456,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein metabolic process") SubClassOf( ) SubClassOf( ) @@ -21421,9 +21465,11 @@ SubClassOf( (organophosphate metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26992"^^xsd:anyURI) AnnotationAssertion( "organophosphate metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019637") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organophosphate metabolic process") SubClassOf( ) SubClassOf( ) @@ -21460,6 +21506,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0019725") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular homeostasis") SubClassOf( ) @@ -21486,8 +21533,10 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019748") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "secondary metabolic process") SubClassOf( ) @@ -21629,7 +21678,7 @@ 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: (neural fold elevation formation) @@ -22110,6 +22159,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0022402") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell cycle process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -22194,25 +22244,31 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022412") AnnotationAssertion(rdfs:label "cellular process involved in reproduction in multicellular organism") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( )) SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +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( ) -SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) # Class: (digestive system process) @@ -22291,6 +22347,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022607") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular component assembly") SubClassOf( ) @@ -22388,6 +22445,7 @@ AnnotationAssertion( "GO:0022892") AnnotationAssertion(Annotation(rdfs:label "Egress of internalized antigen to the cytosol via sec61") "Reactome:R-HSA-1236947") AnnotationAssertion(Annotation(rdfs:label "SLC2A9 transports Fru, Glc, urate") "Reactome:R-HSA-429036") +AnnotationAssertion(Annotation(rdfs:label "MATEs mediate extrusion of xenobiotics") "Reactome:R-HSA-434650") AnnotationAssertion(Annotation(rdfs:label "Defective SLC2A9 does not transport Fru, Glc, urate") "Reactome:R-HSA-5638209") AnnotationAssertion(Annotation(rdfs:label "Fe3+ dissociates from SLC22A17:LCN2:2,5DHBA") "Reactome:R-HSA-5671707") AnnotationAssertion(Annotation(rdfs:label "An unknown carrier transports cytosolic glyoxylate to the peroxisome") "Reactome:R-HSA-6784434") @@ -22503,11 +22561,13 @@ 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") @@ -22822,6 +22882,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell differentiation") SubClassOf( ) @@ -23009,6 +23070,7 @@ AnnotationAssertion( "GO:0030225") AnnotationAssertion(rdfs:label "macrophage differentiation") SubClassOf( ) +SubClassOf( ) # Class: (growth hormone secretion) @@ -23081,7 +23143,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0030299") AnnotationAssertion(rdfs:label "intestinal cholesterol absorption") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -23092,7 +23153,6 @@ AnnotationAssertion( "GO:0030300") AnnotationAssertion(rdfs:label "regulation of intestinal cholesterol absorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -23904,6 +23964,7 @@ AnnotationAssertion( "GO:0031012") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -24532,7 +24593,7 @@ AnnotationAssertion( "regulation of heterochromatin formation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of heterochromatin formation) @@ -24552,7 +24613,7 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of heterochromatin formation) @@ -24571,7 +24632,7 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (heterochromatin formation) @@ -24581,6 +24642,7 @@ AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19112"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22030"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23553"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26702"^^xsd:anyURI) AnnotationAssertion( "GO:0006342") AnnotationAssertion( "GO:0006343") AnnotationAssertion( "GO:0016440") @@ -24608,7 +24670,6 @@ AnnotationAssertion( "GO:0031507") AnnotationAssertion(rdfs:label "heterochromatin formation") SubClassOf( ) -SubClassOf( ) # Class: (motile cilium) @@ -24666,7 +24727,7 @@ AnnotationAssertion( "spindle checkpoint") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0031577") -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 either a mitotic or meiotic child term.") AnnotationAssertion(rdfs:label "spindle checkpoint signaling") SubClassOf( ) @@ -24854,7 +24915,7 @@ AnnotationAssertion( "GO:0031967") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle envelope") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -24866,14 +24927,6 @@ AnnotationAssertion( "membrane-enclosed lumen") SubClassOf( ) -# 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( ) - # Class: (nuclear lumen) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:pz") "The volume enclosed by the nuclear inner membrane.") @@ -25117,7 +25170,7 @@ SubClassOf( ObjectSomeValuesFrom( "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( ))) @@ -25133,7 +25186,7 @@ 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( ))) @@ -25151,7 +25204,7 @@ 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( ))) @@ -25282,16 +25335,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (methylation) - -AnnotationAssertion(Annotation( "GOC:mah") "The process in which a methyl group is covalently attached to a molecule.") -AnnotationAssertion( "Wikipedia:Methylation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0032259") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "methylation") -SubClassOf( ) - # Class: (asymmetric synapse) AnnotationAssertion(Annotation( "GOC:dgh") Annotation( "GOC:ef") "A type of synapse occurring between an axon and a dendritic spine or dendritic shaft. Asymmetric synapses, the most abundant synapse type in the central nervous system, involve axons that contain predominantly spherical vesicles and contain a thickened postsynaptic density. Most or all synapses of this type are excitatory.") @@ -26143,16 +26186,6 @@ AnnotationAssertion(rdfs:label "deve SubClassOf( ) DisjointClasses( ) -# 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: (cytokinetic process) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:isa_complete") Annotation( "GOC:mah") "A cellular process that is involved in cytokinesis (the division of the cytoplasm of a cell and its separation into two daughter cells).") @@ -26286,6 +26319,7 @@ AnnotationAssertion(rdfs:label "RNA SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (negative regulation of ATP-dependent activity) @@ -26378,7 +26412,7 @@ AnnotationAssertion( "negative regulation of epinephrine secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of epinephrine secretion) @@ -26395,7 +26429,7 @@ AnnotationAssertion( "positive regulation of epinephrine secretion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of natural killer cell activation) @@ -26578,9 +26612,11 @@ SubClassOf( ObjectSomeValuesFrom( (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( ) @@ -26785,7 +26821,7 @@ AnnotationAssertion( "GO:0032989") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular anatomical entity morphogenesis") -SubClassOf( ) +SubClassOf( ) # Class: (protein-containing complex) @@ -26800,6 +26836,7 @@ AnnotationAssertion( "GO:0032991") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -27493,7 +27530,7 @@ AnnotationAssertion(owl:deprecated " AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0033554") -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 stress") SubClassOf( ) @@ -28177,7 +28214,6 @@ AnnotationAssertion(rdfs:label "nucl SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (nucleobase-containing compound catabolic process) @@ -28304,7 +28340,6 @@ AnnotationAssertion( "GO:0035036") AnnotationAssertion(rdfs:label "sperm-egg recognition") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (embryonic heart tube development) @@ -28863,7 +28898,6 @@ AnnotationAssertion( "GO:0036093") AnnotationAssertion(rdfs:label "germ cell proliferation") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sperm flagellum) @@ -28978,7 +29012,8 @@ SubClassOf( (cargo receptor activity) -AnnotationAssertion(Annotation( "PMID:15239958") Annotation( "PMID:27903609") "Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span a membrane (either the plasma membrane or a vesicle membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit soluble proteins to nascent vesicles.") +AnnotationAssertion(Annotation( "PMID:15239958") Annotation( "PMID:27903609") "Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span membranes (for instance the plasma membrane or the endoplasmic reticulum membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit the cargo molecules to nascent vesicles.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26872"^^xsd:anyURI) AnnotationAssertion( "bf") AnnotationAssertion( "2011-08-01T02:50:45Z") AnnotationAssertion( "receptor activity") @@ -28996,10 +29031,10 @@ AnnotationAssertion( "GO:0038024") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Notes: (1) this term and its child terms are intended for receptors that bind to and internalize molecules by receptor-mediated endocytosis. For receptors that are coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. (2) Cargo receptors transport substances by vesicular transport, not by transmembrane transport. For transmembrane transporters, consider instead the term 'transmembrane transporter activity ; GO:0022857.") +AnnotationAssertion(rdfs:comment "Notes: (1) For receptors binding a molecule but coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. (2) Cargo receptors transport substances by vesicular transport, not by transmembrane transport. For transmembrane transporters, consider instead the term 'transmembrane transporter activity ; GO:0022857'.") AnnotationAssertion(rdfs:label "cargo receptor activity") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (growth) @@ -29371,11 +29406,12 @@ 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") @@ -29405,6 +29441,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ribosome biogenesis") SubClassOf( ) @@ -30405,10 +30442,12 @@ AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0042995") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell projection") SubClassOf( ) @@ -30503,20 +30542,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (peptide biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.") -AnnotationAssertion( "peptide anabolism") -AnnotationAssertion( "peptide biosynthesis") -AnnotationAssertion( "peptide formation") -AnnotationAssertion( "peptide synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0043043") -AnnotationAssertion(rdfs:label "peptide biosynthetic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - # Class: (obsolete DNA methylation involved in gamete generation) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "PMID:12138111") "OBSOLETE. The covalent transfer of a methyl group to C-5 of cytosine that contributes to the establishment of DNA methylation patterns in the gamete.") @@ -30797,6 +30822,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organelle") SubClassOf( ) @@ -31031,13 +31057,14 @@ AnnotationAssertion( "anoikis") SubClassOf( ) -# 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( )) @@ -31491,22 +31518,14 @@ SubClassOf( (macromolecule modification) AnnotationAssertion(Annotation( "GOC:go_curators") "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043412") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macromolecule modification") SubClassOf( ) -# Class: (macromolecule methylation) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0043414") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "macromolecule methylation") -SubClassOf( ) -SubClassOf( ) - # Class: (positive regulation of skeletal muscle tissue regeneration) AnnotationAssertion(Annotation( "GOC:jl") "Any process that activates or increase the rate of skeletal muscle regeneration.") @@ -31853,15 +31872,6 @@ AnnotationAssertion( "amide metabolic process") SubClassOf( ) -# Class: (amide biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:curators") "The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0043604") -AnnotationAssertion(rdfs:label "amide biosynthetic process") -SubClassOf( ) -SubClassOf( ) - # Class: (keratinocyte proliferation) AnnotationAssertion(Annotation( "CL:0000311") "The multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population. Keratinocytes are epidermal cells which synthesize keratin and undergo a characteristic change as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin.") @@ -31955,16 +31965,6 @@ AnnotationAssertion( "protein-containing complex organization") SubClassOf( ) -# Class: (regulation of DNA methylation) - -AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044030") -AnnotationAssertion(rdfs:label "regulation of DNA methylation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (glucan metabolic process) AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.") @@ -32157,7 +32157,10 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044238") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "primary metabolic process") SubClassOf( ) @@ -32197,12 +32200,15 @@ SubClassOf( (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( ) @@ -32280,6 +32286,7 @@ 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( ) @@ -32338,6 +32345,17 @@ AnnotationAssertion( "neuron spine") SubClassOf( ) +# Class: (response to leptin) + +AnnotationAssertion(Annotation( "GOC:yaf") "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 leptin stimulus. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body. It plays a key role in regulating energy intake and energy expenditure, including appetite and metabolism].") +AnnotationAssertion( "jl") +AnnotationAssertion( "2010-07-14T02:31:20Z") +AnnotationAssertion(Annotation( "GOC:dos") "response to leptin stimulus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0044321") +AnnotationAssertion(rdfs:label "response to leptin") +SubClassOf( ) + # Class: (type B pancreatic cell proliferation) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:yaf") "The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin.") @@ -32524,7 +32542,7 @@ AnnotationAssertion( "2014-07-16T13:12:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044848") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase.") AnnotationAssertion(rdfs:label "biological phase") SubClassOf( ) @@ -32827,6 +32845,7 @@ AnnotationAssertion(Annotation( "GO:0045202") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -34261,7 +34280,6 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -34567,7 +34585,6 @@ AnnotationAssertion( "negative regulation of intestinal cholesterol absorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -34584,7 +34601,6 @@ AnnotationAssertion( "positive regulation of intestinal cholesterol absorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -36037,9 +36053,11 @@ SubClassOf( (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( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "heterocycle metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0046483") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "heterocycle metabolic process") SubClassOf( ) @@ -37004,7 +37022,8 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048241") AnnotationAssertion(rdfs:label "epinephrine transport") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (epinephrine secretion) @@ -37013,8 +37032,8 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048242") AnnotationAssertion(rdfs:label "epinephrine secretion") -SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (norepinephrine secretion) @@ -37430,7 +37449,7 @@ SubClassOf( ObjectSomeValuesFrom( "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( ))) @@ -37447,7 +37466,7 @@ 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( ))) @@ -37464,7 +37483,7 @@ 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( ))) @@ -37553,13 +37572,15 @@ 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: (regulation of muscle organ development) @@ -38405,6 +38426,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anatomical structure development") SubClassOf( ) @@ -38414,8 +38436,8 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0048858") AnnotationAssertion(rdfs:label "cell projection morphogenesis") +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (stem cell differentiation) @@ -38457,6 +38479,7 @@ AnnotationAssertion( "GO:0048870") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell motility") @@ -39374,6 +39397,8 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of T cell activation) AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of T cell activation.") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "positive regulation of T lymphocyte activation") AnnotationAssertion( "positive regulation of T-cell activation") AnnotationAssertion( "positive regulation of T-lymphocyte activation") @@ -39469,6 +39494,7 @@ 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") @@ -39521,11 +39547,11 @@ SubClassOf( (intestinal absorption) -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") "Any process in which nutrients are taken up from the contents of the intestine.") +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dph") "A process in which nutrients are taken up from the contents of the intestine.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26825"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050892") AnnotationAssertion(rdfs:label "intestinal absorption") -SubClassOf( ) SubClassOf( ) # Class: (response to stimulus) @@ -39535,12 +39561,13 @@ 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( ) @@ -40406,6 +40433,7 @@ SubClassOf( ObjectSomeValuesFrom( (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") @@ -40419,6 +40447,7 @@ AnnotationAssertion( "GOC:TermGenie") "single organism localization") AnnotationAssertion( "single-organism localization") AnnotationAssertion( "GO:0051179") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "localization") SubClassOf( ) @@ -40868,7 +40897,6 @@ 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( ))) @@ -40958,7 +40986,6 @@ 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( ))) @@ -40977,7 +41004,6 @@ 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( ))) @@ -41646,7 +41672,7 @@ 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( ) @@ -42073,7 +42099,6 @@ AnnotationAssertion( "GO:0051955") AnnotationAssertion(rdfs:label "regulation of amino acid transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42089,7 +42114,6 @@ AnnotationAssertion( "GO:0051956") AnnotationAssertion(rdfs:label "negative regulation of amino acid transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42107,7 +42131,6 @@ AnnotationAssertion( "GO:0051957") AnnotationAssertion(rdfs:label "positive regulation of amino acid transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42426,6 +42449,7 @@ AnnotationAssertion( "GO:0055085") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -42560,7 +42584,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0060011") AnnotationAssertion(rdfs:label "Sertoli cell proliferation") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -42816,9 +42839,12 @@ AnnotationAssertion( "protein-containing complex scaffold activity") AnnotationAssertion( "GO:0060090") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "molecular adaptor activity") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43782,7 +43808,6 @@ AnnotationAssertion( "GO:0060468") AnnotationAssertion(rdfs:label "prevention of polyspermy") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -43807,7 +43832,6 @@ AnnotationAssertion( "protein localization involved in acrosome reaction") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -44557,13 +44581,12 @@ SubClassOf( (intestinal phytosterol absorption) -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process in which phytosterols are taken up from the contents of the intestine.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "A process in which phytosterols are taken up from the contents of the intestine.") AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-22T02:08:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060752") AnnotationAssertion(rdfs:label "intestinal phytosterol absorption") -SubClassOf( ) SubClassOf( ) # Class: (regulation of branching involved in mammary gland duct morphogenesis) @@ -44602,7 +44625,6 @@ AnnotationAssertion( "GO:0060767") AnnotationAssertion(rdfs:label "epithelial cell proliferation involved in prostate gland development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -44616,7 +44638,6 @@ AnnotationAssertion( "regulation of epithelial cell proliferation involved in prostate gland development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of epithelial cell proliferation involved in prostate gland development) @@ -44660,7 +44681,6 @@ AnnotationAssertion( "mesenchymal cell proliferation involved in prostate gland development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of mesenchymal cell proliferation involved in prostate gland development) @@ -44673,7 +44693,6 @@ AnnotationAssertion( "regulation of mesenchymal cell proliferation involved in prostate gland development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cell proliferation involved in tissue homeostasis) @@ -46864,17 +46883,6 @@ AnnotationAssertion(rdfs:label "inte SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (heterochromatin organization) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2009-07-23T04:12:48Z") -AnnotationAssertion(Annotation( "GOC:mah") "heterochromatin organisation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0070828") -AnnotationAssertion(rdfs:label "heterochromatin organization") -SubClassOf( ) - # Class: (regulation of glycogen metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen.") @@ -46928,7 +46936,7 @@ AnnotationAssertion( "2009-08-27T04:41:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070887") -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 chemical stimulus") SubClassOf( ) @@ -47001,7 +47009,7 @@ AnnotationAssertion( "spindle assembly checkpoint") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071173") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to specify the type of spindle assembly checkpoint (mitotic or meiotic).") AnnotationAssertion(rdfs:label "spindle assembly checkpoint signaling") SubClassOf( ) @@ -47021,7 +47029,7 @@ AnnotationAssertion( "topo II checkpoint") AnnotationAssertion( "topoisomerase II checkpoint") AnnotationAssertion( "GO:0071174") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to specify the type of spindle checkpoint (assembly, orientation checkpoints).") AnnotationAssertion(rdfs:label "mitotic spindle checkpoint signaling") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -47036,7 +47044,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GOC:mah") "cellular response to abiotic stress") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071214") -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 abiotic stimulus") SubClassOf( ) @@ -47318,6 +47326,7 @@ AnnotationAssertion( "2010-03-08T03:56:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071705") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nitrogen compound transport") SubClassOf( ) @@ -47576,6 +47585,7 @@ AnnotationAssertion(rdfs:label "DNA SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (cell periphery) @@ -48687,7 +48697,7 @@ 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( ))) @@ -48924,7 +48934,7 @@ AnnotationAssertion( "GO:0090141") AnnotationAssertion(rdfs:label "positive regulation of mitochondrial fission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -49105,7 +49115,7 @@ AnnotationAssertion( "2010-01-20T10:29:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090231") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to specify the type of checkpoint (i.e mitotic spindle or DNA damage etc).") AnnotationAssertion(rdfs:label "regulation of spindle checkpoint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -49120,7 +49130,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "spindle checkpoint activation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090232") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "positive regulation of spindle checkpoint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -49135,7 +49145,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "spindle checkpoint silencing") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090233") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to specify the type of checkpoint (i.e mitotic spindle or DNA damage etc).") AnnotationAssertion(rdfs:label "negative regulation of spindle checkpoint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -49165,7 +49175,7 @@ AnnotationAssertion( "GO:0090258") AnnotationAssertion(rdfs:label "negative regulation of mitochondrial fission") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -49302,10 +49312,13 @@ SubClassOf( ObjectSomeValuesFrom( "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") SubClassOf( ) SubClassOf( ) @@ -50220,7 +50233,7 @@ 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( ))) @@ -50444,9 +50457,11 @@ SubClassOf( "GOC:dos") "Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098754") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "detoxification") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -50530,7 +50545,7 @@ AnnotationAssertion(Annotation( "cellular_component") AnnotationAssertion( "mitochondrial protein complex") AnnotationAssertion( "GO:0098798") -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 "mitochondrial protein-containing complex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -50613,11 +50628,10 @@ SubClassOf( (intestinal lipid absorption) -AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:sl") Annotation( "PMID:18768481") "Any process in which lipids are taken up from the contents of the intestine.") +AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:sl") Annotation( "PMID:18768481") "A process in which lipids are taken up from the contents of the intestine.") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098856") AnnotationAssertion(rdfs:label "intestinal lipid absorption") -SubClassOf( ) SubClassOf( ) # Class: (membrane microdomain) @@ -51116,7 +51130,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0106001") AnnotationAssertion(rdfs:label "intestinal hexose absorption") -SubClassOf( ) SubClassOf( ) # Class: (regulation of inflammatory response to wounding) @@ -51502,7 +51515,6 @@ AnnotationAssertion( "GO:0120211") AnnotationAssertion(rdfs:label "proacrosomal vesicle fusion") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of blastocyst development) @@ -51531,56 +51543,6 @@ AnnotationAssertion( "olefinic compound metabolic process") SubClassOf( ) -# Class: (regulation of heterochromatin organization) - -AnnotationAssertion(Annotation( "GOC:krc") "Any process that modulates the frequency, rate, extent or location of heterochromatin organization.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20020"^^xsd:anyURI) -AnnotationAssertion( "krc") -AnnotationAssertion( "2020-09-29T20:00:04Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0120261") -AnnotationAssertion(rdfs:label "regulation of heterochromatin organization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of heterochromatin organization) - -AnnotationAssertion(Annotation( "GOC:krc") "Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin organization.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20020"^^xsd:anyURI) -AnnotationAssertion( "krc") -AnnotationAssertion( "2020-09-29T20:12:30Z") -AnnotationAssertion( "down regulation of heterochromatin organization") -AnnotationAssertion( "down-regulation of heterochromatin organization") -AnnotationAssertion( "downregulation of heterochromatin organization") -AnnotationAssertion( "inhibition of heterochromatin organization") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0120262") -AnnotationAssertion(rdfs:label "negative regulation of heterochromatin organization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of heterochromatin organization) - -AnnotationAssertion(Annotation( "GOC:krc") "Any process that activates or increases the frequency, rate or extent of heterochromatin organization.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20020"^^xsd:anyURI) -AnnotationAssertion( "krc") -AnnotationAssertion( "2020-09-29T20:19:19Z") -AnnotationAssertion( "up regulation of heterochromatin organization") -AnnotationAssertion( "up-regulation of heterochromatin organization") -AnnotationAssertion( "upregulation of heterochromatin organization") -AnnotationAssertion( "activation of heterochromatin organization") -AnnotationAssertion( "stimulation of heterochromatin organization") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0120263") -AnnotationAssertion(rdfs:label "positive regulation of heterochromatin organization") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of pigmentation) AnnotationAssertion(Annotation( "GOC:krc") "Any process that modulates the frequency, rate or extent of the deposition or modulates the distribution of coloring matter in an organism.") @@ -51858,7 +51820,7 @@ SubClassOf( (P-type transmembrane transporter activity) -AnnotationAssertion(Annotation( "PMID:18075584") Annotation( "PMID:25918123") "Primary active transporter that auto-phosphorylates (hence P) at a key conserved aspartate residue, generating a conformational change that allows transport of the substrate. Hydrolysis of the phosphorylated Asp residue, catalyzed by the actuator (A) domain, results in another state with occluded substrates. Upon dissociation of Mg2+ and inorganic phosphate (Pi), the enzyme reverts to the initial state, in which the counter-transported substrate is released into the cytosol.") +AnnotationAssertion(Annotation( "PMID:18075584") Annotation( "PMID:25918123") "Primary active transporter that auto-phosphorylates (hence P) at a key conserved aspartate residue, generating a conformational change that allows transport of the substrate. Hydrolysis of the phosphorylated Asp residue, catalyzed by the actuator (A) domain, results in another state with occluded substrates. Upon dissociation of Mg2+ and Pi, the enzyme reverts to the initial state, in which the counter-transported substrate is released into the cytosol.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20529"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21273"^^xsd:anyURI) AnnotationAssertion( "pg") @@ -52050,6 +52012,19 @@ AnnotationAssertion(rdfs:label "mult SubClassOf( ) SubClassOf( ) +# 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") +SubClassOf( ) + # Class: (distal axon) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:17202468") "That part of an axon close to and including the growth cone or the axon terminus.") @@ -53802,6 +53777,7 @@ SubClassOf( (organonitrogen compound catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-04T15:17:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound breakdown") @@ -53809,6 +53785,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound degradation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901565") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organonitrogen compound catabolic process") SubClassOf( ) SubClassOf( ) @@ -53816,6 +53793,7 @@ SubClassOf( (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") @@ -53824,6 +53802,7 @@ AnnotationAssertion(Annotation( "GOC:TermGenie") "organonitrogen compound synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901566") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organonitrogen compound biosynthetic process") SubClassOf( ) SubClassOf( ) @@ -53857,17 +53836,16 @@ SubClassOf( (organic substance catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-05T11:04:36Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity breakdown") AnnotationAssertion( "organic molecular entity catabolic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity catabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity degradation") AnnotationAssertion( "organic substance breakdown") AnnotationAssertion( "organic substance catabolism") AnnotationAssertion( "organic substance degradation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901575") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic substance catabolic process") SubClassOf( ) SubClassOf( ) @@ -53875,6 +53853,7 @@ 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") @@ -53888,6 +53867,7 @@ AnnotationAssertion( "organic substance synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901576") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic substance biosynthetic process") SubClassOf( ) SubClassOf( ) @@ -54272,9 +54252,11 @@ AnnotationAssertion( "GO:1901860") AnnotationAssertion(rdfs:label "positive regulation of mitochondrial DNA metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cell junction assembly) @@ -54498,7 +54480,7 @@ AnnotationAssertion( "GOC:obol") "regulation of G1/S checkpoint") AnnotationAssertion( "regulation of G1/S transition checkpoint") AnnotationAssertion( "GO:1901976") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to specify the type of checkpoint (i.e mitotic spindle or DNA damage etc).") AnnotationAssertion(rdfs:label "regulation of cell cycle checkpoint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -54520,7 +54502,7 @@ AnnotationAssertion( "GOC:obol") "negative regulation of G1/S checkpoint") AnnotationAssertion( "negative regulation of G1/S transition checkpoint") AnnotationAssertion( "GO:1901977") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to specify the type of checkpoint (i.e mitotic spindle or DNA damage etc).") AnnotationAssertion(rdfs:label "negative regulation of cell cycle checkpoint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -57116,7 +57098,7 @@ AnnotationAssertion( "negative regulation of autophagy of mitochondrion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -58262,7 +58244,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of mitotic cell cycle spindle checkpoint") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903504") -AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to specify the type of spindle checkpoint (assembly, orientation or Dma1-dependent).") AnnotationAssertion(rdfs:label "regulation of mitotic spindle checkpoint") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -58569,7 +58551,7 @@ AnnotationAssertion(rdfs:comment "An AnnotationAssertion(rdfs:label "positive regulation of autophagy of mitochondrion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -59969,7 +59951,6 @@ AnnotationAssertion( "regulation of intestinal absorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of intestinal absorption) @@ -59985,7 +59966,6 @@ AnnotationAssertion( "GO:1904479") AnnotationAssertion(rdfs:label "negative regulation of intestinal absorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -60003,7 +59983,6 @@ AnnotationAssertion( "GO:1904480") AnnotationAssertion(rdfs:label "positive regulation of intestinal absorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -60373,7 +60352,6 @@ AnnotationAssertion( "GO:1904729") AnnotationAssertion(rdfs:label "regulation of intestinal lipid absorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -60390,7 +60368,6 @@ AnnotationAssertion( "GO:1904730") AnnotationAssertion(rdfs:label "negative regulation of intestinal lipid absorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -60408,7 +60385,6 @@ AnnotationAssertion( "GO:1904731") AnnotationAssertion(rdfs:label "positive regulation of intestinal lipid absorption") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -61421,7 +61397,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:1905198") AnnotationAssertion(rdfs:label "manchette assembly") -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -61434,7 +61409,6 @@ AnnotationAssertion( "GO:1905199") AnnotationAssertion(rdfs:label "manchette disassembly") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of cardiocyte differentiation) @@ -61997,6 +61971,7 @@ AnnotationAssertion( AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905517") AnnotationAssertion(rdfs:label "macrophage migration") +SubClassOf( ) SubClassOf( ) # Class: (regulation of macrophage migration) @@ -62008,7 +61983,7 @@ AnnotationAssertion( "GO:1905521") AnnotationAssertion(rdfs:label "regulation of macrophage migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of macrophage migration) @@ -62024,7 +61999,7 @@ AnnotationAssertion( "GO:1905522") AnnotationAssertion(rdfs:label "negative regulation of macrophage migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -62041,7 +62016,7 @@ AnnotationAssertion( "GO:1905523") AnnotationAssertion(rdfs:label "positive regulation of macrophage migration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -62185,40 +62160,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of DNA methylation) - -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:27336847") "Any process that stops, prevents or reduces the frequency, rate or extent of DNA methylation.") -AnnotationAssertion( "bc") -AnnotationAssertion( "2016-11-04T16:43:13Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of DNA methylation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of DNA methylation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of DNA methylation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of DNA methylation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905642") -AnnotationAssertion(rdfs:label "negative regulation of DNA methylation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of DNA methylation) - -AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:27336847") "Any process that activates or increases the frequency, rate or extent of DNA methylation.") -AnnotationAssertion( "bc") -AnnotationAssertion( "2016-11-04T16:43:22Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of DNA methylation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of DNA methylation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of DNA methylation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of DNA methylation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1905643") -AnnotationAssertion(rdfs:label "positive regulation of DNA methylation") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of artery morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:27389411") "Any process that modulates the frequency, rate or extent of artery morphogenesis.") @@ -62572,7 +62513,6 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of germ cell proliferation) @@ -62591,7 +62531,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of germ cell proliferation) @@ -62610,7 +62549,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of gonad development) @@ -63505,6 +63443,7 @@ AnnotationAssertion( "negative regulation of male germ cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -63518,6 +63457,7 @@ AnnotationAssertion( "positive regulation of male germ cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -63879,7 +63819,6 @@ AnnotationAssertion( "regulation of ovarian follicle development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of ovarian follicle development) @@ -63893,7 +63832,6 @@ AnnotationAssertion( "negative regulation of ovarian follicle development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -63908,7 +63846,6 @@ AnnotationAssertion( "regulation of binding of sperm to zona pellucida") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of binding of sperm to zona pellucida) @@ -64013,7 +63950,6 @@ AnnotationAssertion( "positive regulation of ovarian follicle development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) diff --git a/src/ontology/imports/mpath_import.owl b/src/ontology/imports/mpath_import.owl index e5185144..83a4caa4 100644 --- a/src/ontology/imports/mpath_import.owl +++ b/src/ontology/imports/mpath_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-01") +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/nbo_import.owl b/src/ontology/imports/nbo_import.owl index 298459df..d8551b16 100644 --- a/src/ontology/imports/nbo_import.owl +++ b/src/ontology/imports/nbo_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-01") +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index c9fa15a1..5ee7e6b6 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-01") +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pr_import.owl b/src/ontology/imports/pr_import.owl index 59154f76..2e94ecfb 100644 --- a/src/ontology/imports/pr_import.owl +++ b/src/ontology/imports/pr_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-01") +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 0b08b9d8..e4c113c2 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-01") +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index a2bcab42..2d71bda2 100644 --- a/src/ontology/imports/uberon_import.owl +++ b/src/ontology/imports/uberon_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( ) Annotation( ) @@ -68,7 +68,7 @@ Annotation( "PMID:16417468 Forgotten and Annotation( "aggregates AAO from 13:04:2012") Annotation( "aggregates TAO from 09:08:2012") Annotation( "aggregates VSAO from 16:07:2012") -Annotation(owl:versionInfo "2024-04-01") +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) Declaration(Class()) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 905efe25..bba94a68 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-04-01") + +Annotation(owl:versionInfo "2024-04-17") Declaration(Class()) Declaration(Class())