diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index c9af9d1..a66d683 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -7,21 +7,17 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-18") +Annotation(owl:versionInfo "2024-08-18") Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -57,47 +53,5 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "entity"@en) -# Class: (continuant) - -AnnotationAssertion( "continuant") -AnnotationAssertion( "Continuant") -AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) -AnnotationAssertion(Annotation( ) "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) -AnnotationAssertion(Annotation( ) "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) -AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])"@en) -AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])"@en) -AnnotationAssertion(Annotation( ) "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ") -AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ) - -# Class: (independent continuant) - -AnnotationAssertion( "ic") -AnnotationAssertion( "IndependentContinuant") -AnnotationAssertion( "a chair"@en) -AnnotationAssertion( "a heart"@en) -AnnotationAssertion( "a leg"@en) -AnnotationAssertion( "a molecule"@en) -AnnotationAssertion( "a spatial region"@en) -AnnotationAssertion( "an atom"@en) -AnnotationAssertion( "an orchestra."@en) -AnnotationAssertion( "an organism"@en) -AnnotationAssertion( "the bottom right portion of a human torso"@en) -AnnotationAssertion( "the interior of your mouth"@en) -AnnotationAssertion(Annotation( ) "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) -AnnotationAssertion(Annotation( ) "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])"@en) -AnnotationAssertion(Annotation( ) "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") -AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") -AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "independent continuant"@en) -SubClassOf( ) - ) \ No newline at end of file diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl index f1975e7..15444d1 100644 --- a/src/ontology/imports/chebi_import.owl +++ b/src/ontology/imports/chebi_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-04-18") + +Annotation(owl:versionInfo "2024-08-18") Declaration(Class()) Declaration(ObjectProperty()) diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index bdd9c53..e6a9735 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-04-18") + +Annotation( ) +Annotation(owl:versionInfo "2024-08-18") Declaration(Class()) Declaration(Class()) @@ -31,6 +31,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -188,7 +189,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -207,7 +207,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -346,7 +345,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -440,7 +438,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -455,13 +452,14 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -632,7 +630,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -763,8 +760,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -847,11 +844,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -969,9 +966,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1051,6 +1045,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1159,7 +1154,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1168,8 +1162,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1315,12 +1307,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1854,7 +1842,7 @@ SubClassOf( (mitotic cell cycle) -AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0815316194") Annotation( "Reactome:69278") "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.") +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0815316194") "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.") AnnotationAssertion( "GO:0007067") AnnotationAssertion( "Wikipedia:Mitosis") AnnotationAssertion( "biological_process") @@ -2016,6 +2004,25 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of cell growth by extracellular stimulus) + +AnnotationAssertion(Annotation( "GOC:dph") "Any process in which external signals modulate the frequency, rate or extent of cell growth, the irreversible increase in size of a cell over time.") +AnnotationAssertion( "interpretation of external signals that regulate cell growth") +AnnotationAssertion( "regulation of cell growth by detection of exogenous stimulus") +AnnotationAssertion( "regulation of cell growth by sensing of exogenous stimulus") +AnnotationAssertion( "regulation of growth by exogenous signal") +AnnotationAssertion( "regulation of growth by exogenous stimuli") +AnnotationAssertion( "regulation of growth by exogenous stimulus") +AnnotationAssertion( "regulation of growth by external signal") +AnnotationAssertion( "regulation of growth by external stimuli") +AnnotationAssertion( "regulation of growth by external stimulus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0001560") +AnnotationAssertion(rdfs:label "regulation of cell growth by extracellular stimulus") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (microtubule bundle formation) AnnotationAssertion(Annotation( "GOC:dph") "A process that results in a parallel arrangement of microtubules.") @@ -2242,6 +2249,7 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of protein phosphorylation) AnnotationAssertion(Annotation( "GOC:hjd") "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:bf") "positive regulation of protein amino acid phosphorylation") AnnotationAssertion( "up regulation of protein amino acid phosphorylation") AnnotationAssertion( "up-regulation of protein amino acid phosphorylation") @@ -2250,6 +2258,7 @@ AnnotationAssertion( "stimulation of protein amino acid phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0001934") +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "positive regulation of protein phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -2259,7 +2268,7 @@ SubClassOf( ObjectSomeValuesFrom( (heart looping) -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12094232") "The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12094232") "The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceding septation.") AnnotationAssertion( "cardiac looping") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0001947") @@ -3663,9 +3672,10 @@ SubClassOf( (all-trans-retinol dehydrogenase (NAD+) activity) -AnnotationAssertion(Annotation( "RHEA:21284") "Catalysis of the reaction: retinol + NAD+ = retinal + NADH + H+.") +AnnotationAssertion(Annotation( "RHEA:48488") "Catalysis of the reaction: all-trans-retinol--[retinol-binding protein] + NAD+ = all-trans-retinal--[retinol-binding protein] + H+ + NADH. Recognizes the substrate both in free form and when bound to cellular-retinol-binding-protein (CRBP1), but has higher affinity for the bound form.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20980"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27136"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28011"^^xsd:anyURI) AnnotationAssertion(Annotation( "EC:1.1.1.105") "all-trans retinol dehydrogenase activity") AnnotationAssertion(Annotation( "GOC:ecd") Annotation( "PMID:12036956") "retinal reductase activity") AnnotationAssertion(Annotation( "EC:1.1.1.105") "retinene reductase activity") @@ -3673,7 +3683,7 @@ AnnotationAssertion(Annotation( "retinol dehydrogenase activity") AnnotationAssertion( "EC:1.1.1.105") AnnotationAssertion( "MetaCyc:RETINOL-DEHYDROGENASE-RXN") -AnnotationAssertion( "RHEA:21284") +AnnotationAssertion( "RHEA:48488") AnnotationAssertion(Annotation(rdfs:label "RDH5 oxidises 11cROL to 11cRAL") "Reactome:R-HSA-2454081") AnnotationAssertion(Annotation(rdfs:label "Defective RDH5 does not oxidise 11cROL to 11cRAL and causes RPA") "Reactome:R-HSA-2466832") AnnotationAssertion(Annotation(rdfs:label "RDH10,16,DHRS9,RDHE2 oxidise atROL to atRAL") "Reactome:R-HSA-5362518") @@ -3933,7 +3943,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "carbohydrate metabolic process") SubClassOf( ) -SubClassOf( ) # Class: (disaccharide metabolic process) @@ -4102,7 +4111,6 @@ AnnotationAssertion( "organic acid metabolic process") SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (lactate metabolic process) @@ -4237,11 +4245,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nucleobase-containing compound metabolic process") -SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) # Class: (regulation of nucleotide metabolic process) @@ -4592,7 +4596,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino acid metabolic process") SubClassOf( ) -SubClassOf( ) # Class: (regulation of cellular amino acid metabolic process) @@ -4658,16 +4661,19 @@ AnnotationAssertion( "glycine metabolic process") SubClassOf( ) -# Class: (histidine metabolic process) +# Class: (L-histidine metabolic process) -AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.") +AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.") +AnnotationAssertion( "histidine metabolic process") AnnotationAssertion( "Wikipedia:Histidine") AnnotationAssertion( "histidine metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006547") -AnnotationAssertion(rdfs:label "histidine metabolic process") -SubClassOf( ) -SubClassOf( ) +AnnotationAssertion(rdfs:label "L-histidine metabolic process") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (isoleucine metabolic process) @@ -4892,7 +4898,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lipid metabolic process") SubClassOf( ) -SubClassOf( ) # Class: (fatty acid metabolic process) @@ -4935,18 +4940,6 @@ AnnotationAssertion( "icosanoid metabolic process") SubClassOf( ) -# Class: (cellular aromatic compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.") -AnnotationAssertion( "aromatic compound metabolism") -AnnotationAssertion( "aromatic hydrocarbon metabolic process") -AnnotationAssertion( "aromatic hydrocarbon metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0006725") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular aromatic compound metabolic process") -SubClassOf( ) - # Class: (NADH metabolic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0618254153") "The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.") @@ -5051,18 +5044,16 @@ AnnotationAssertion( "phosphate-containing compound metabolic process") SubClassOf( ) -# Class: (nitrogen compound metabolic process) +# Class: (obsolete nitrogen compound metabolic process) -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.") +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "nitrogen compound metabolism") +AnnotationAssertion( "GO:0008152") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006807") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "nitrogen compound metabolic process") -SubClassOf( ) +AnnotationAssertion(rdfs:comment "The reason for obsoletion is that this term was an unnecessary grouping term.") +AnnotationAssertion(rdfs:label "obsolete nitrogen compound metabolic process") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Class: (transport) @@ -5155,7 +5146,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amino acid transport") -SubClassOf( ) +SubClassOf( ) # Class: (cell volume homeostasis) @@ -5206,19 +5197,6 @@ AnnotationAssertion( "apoptotic process") SubClassOf( ) -# Class: (obsolete movement of cell or subcellular component) - -AnnotationAssertion(Annotation( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:mlg") "OBSOLETE. The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19809"^^xsd:anyURI) -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jl") "cellular component motion") -AnnotationAssertion( "cellular component movement") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "cell movement") -AnnotationAssertion( "GO:0006928") -AnnotationAssertion(rdfs:comment "This term was obsoleted because it mixes cellular and subcellular processes.") -AnnotationAssertion(rdfs:label "obsolete movement of cell or subcellular component") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) - # Class: (chemotaxis) AnnotationAssertion(Annotation( "ISBN:0198506732") "The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).") @@ -5282,6 +5260,7 @@ SubClassOf( ObjectSomeValuesFrom( (organelle organization) AnnotationAssertion(Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-19T15:25:51Z") AnnotationAssertion( "GO:1902589") @@ -5291,8 +5270,10 @@ AnnotationAssertion( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:mah") "organelle organization and biogenesis") AnnotationAssertion( "single-organism organelle organization") AnnotationAssertion( "GO:0006996") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "organelle organization") SubClassOf( ) @@ -5561,7 +5542,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell surface receptor signaling pathway) 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") @@ -6082,7 +6062,6 @@ AnnotationAssertion( "GO:0008202") AnnotationAssertion(rdfs:label "steroid metabolic process") SubClassOf( ) -SubClassOf( ) # Class: (cholesterol metabolic process) @@ -6259,7 +6238,7 @@ AnnotationAssertion( "GO:0008610") AnnotationAssertion(rdfs:label "lipid biosynthetic process") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (guanosine metabolic process) @@ -6320,6 +6299,7 @@ SubClassOf( "GOC:mah") "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15249"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25418"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "GO:0043284") AnnotationAssertion(Annotation( "GOC:mtg_chebi_dec09") "biopolymer biosynthetic process") AnnotationAssertion( "macromolecule anabolism") @@ -6328,11 +6308,12 @@ AnnotationAssertion( "macromolecule synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0009059") +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "macromolecule biosynthetic process") SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (glutamine family amino acid metabolic process) @@ -6373,9 +6354,7 @@ AnnotationAssertion( "GO:0009072") AnnotationAssertion(rdfs:label "aromatic amino acid metabolic process") SubClassOf( ) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (pyruvate family amino acid metabolic process) @@ -6703,13 +6682,14 @@ SubClassOf( "GOC:jl") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(Annotation( "GOC:dos") "response to hormone stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "growth regulator") AnnotationAssertion( "GO:0009725") AnnotationAssertion(rdfs:label "response to hormone") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (detection of endogenous stimulus) @@ -7093,24 +7073,16 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "cellular process") SubClassOf( ) -# Class: (response to organic substance) - -AnnotationAssertion(Annotation( "GOC:sm") Annotation( "PMID:23356676") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.") -AnnotationAssertion( "GO:1990367") -AnnotationAssertion( "process resulting in tolerance to organic substance") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0010033") -AnnotationAssertion(rdfs:label "response to organic substance") -SubClassOf( ) - # Class: (response to organonitrogen compound) AnnotationAssertion(Annotation( "PMID:9869419") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "response to organic nitrogen") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010243") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "response to organonitrogen compound") -SubClassOf( ) SubClassOf( ) # Class: (negative regulation of peptidase activity) @@ -7801,7 +7773,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0015695") AnnotationAssertion(rdfs:label "organic cation transport") -SubClassOf( ) +SubClassOf( ) # Class: (organic anion transport) @@ -7809,7 +7781,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0015711") AnnotationAssertion(rdfs:label "organic anion transport") -SubClassOf( ) +SubClassOf( ) # Class: (methionine transport) @@ -7820,6 +7792,7 @@ AnnotationAssertion( "methionine transport") SubClassOf( ) SubClassOf( ) +SubClassOf( ) # Class: (amine transport) @@ -7829,7 +7802,6 @@ AnnotationAssertion( "GO:0015837") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amine transport") -SubClassOf( ) SubClassOf( ) # Class: (cadaverine transport) @@ -7848,7 +7820,7 @@ AnnotationAssertion( "GO:0015849") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic acid transport") -SubClassOf( ) +SubClassOf( ) # Class: (energy derivation by oxidation of organic compounds) @@ -7943,7 +7915,7 @@ AnnotationAssertion( "GO:0016051") AnnotationAssertion(rdfs:label "carbohydrate biosynthetic process") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (carbohydrate catabolic process) @@ -7964,7 +7936,7 @@ AnnotationAssertion( "GO:0016052") AnnotationAssertion(rdfs:label "carbohydrate catabolic process") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (organic acid biosynthetic process) @@ -7979,7 +7951,6 @@ AnnotationAssertion(rdfs:label "orga SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (Wnt signaling pathway) @@ -8186,13 +8157,10 @@ SubClassOf( (oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor) -AnnotationAssertion(Annotation( "EC:1.1.1.-") Annotation( "GOC:ai") "Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.") +AnnotationAssertion(Annotation( "EC:1.1.1.-") "Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.") AnnotationAssertion( "EC:1.1.1.-") AnnotationAssertion(Annotation(rdfs:label "RDH11 reduces RBP2:atRAL to RBP2:atROL") "Reactome:R-HSA-975629") AnnotationAssertion( "molecular_function") -AnnotationAssertion( "NADH-dependent glyoxylate reductase") -AnnotationAssertion(Annotation( "EC:1.1.1.26") "glycolate reductase") -AnnotationAssertion( "glyoxylic acid reductase") AnnotationAssertion( "GO:0016616") AnnotationAssertion(rdfs:label "oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor") SubClassOf( ) @@ -8370,19 +8338,6 @@ AnnotationAssertion( "oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor") SubClassOf( ) -# Class: (heterocycle biosynthetic process) - -AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).") -AnnotationAssertion( "heterocycle anabolism") -AnnotationAssertion( "heterocycle biosynthesis") -AnnotationAssertion( "heterocycle formation") -AnnotationAssertion( "heterocycle synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0018130") -AnnotationAssertion(rdfs:label "heterocycle biosynthetic process") -SubClassOf( ) -SubClassOf( ) - # Class: (peptidyl-amino acid modification) AnnotationAssertion(Annotation( "GOC:mah") "The alteration of an amino acid residue in a peptide.") @@ -8463,8 +8418,6 @@ AnnotationAssertion( "GO:0018958") AnnotationAssertion(rdfs:comment "Note that phenol metabolism is not included as a child of 'xenobiotic metabolism' because although it is synthesized industrially, phenol is also found naturally in animal wastes and other organic materials. It is often formed by the activity of microorganisms, which can chemically modify a variety of xenobiotic and naturally occurring phenolic compounds.") AnnotationAssertion(rdfs:label "phenol-containing compound metabolic process") -SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (reproductive behavior) @@ -8532,8 +8485,6 @@ AnnotationAssertion(Annotation( "GO:0019219") AnnotationAssertion(rdfs:label "regulation of nucleobase-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -8563,6 +8514,20 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (mannose catabolic process) + +AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the breakdown of mannose, the aldohexose manno-hexose, the C-2 epimer of glucose.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27107"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27638"^^xsd:anyURI) +AnnotationAssertion( "mannose breakdown") +AnnotationAssertion( "mannose catabolism") +AnnotationAssertion( "mannose degradation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0019309") +AnnotationAssertion(rdfs:label "mannose catabolic process") +SubClassOf( ) +SubClassOf( ) + # Class: (hexose metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.") @@ -8585,6 +8550,18 @@ AnnotationAssertion(rdfs:label "hexo SubClassOf( ) SubClassOf( ) +# Class: (hexose catabolic process) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule.") +AnnotationAssertion( "hexose breakdown") +AnnotationAssertion( "hexose catabolism") +AnnotationAssertion( "hexose degradation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0019320") +AnnotationAssertion(rdfs:label "hexose catabolic process") +SubClassOf( ) +SubClassOf( ) + # Class: (pentose metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving a pentose, any monosaccharide with a chain of five carbon atoms in the molecule.") @@ -8627,21 +8604,6 @@ AnnotationAssertion(rdfs:label "aldi SubClassOf( ) SubClassOf( ) -# Class: (aromatic compound biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.") -AnnotationAssertion( "aromatic compound anabolism") -AnnotationAssertion( "aromatic compound biosynthesis") -AnnotationAssertion( "aromatic compound formation") -AnnotationAssertion( "aromatic compound synthesis") -AnnotationAssertion( "aromatic hydrocarbon biosynthesis") -AnnotationAssertion( "aromatic hydrocarbon biosynthetic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0019438") -AnnotationAssertion(rdfs:label "aromatic compound biosynthetic process") -SubClassOf( ) -SubClassOf( ) - # Class: (pyridine metabolic process) AnnotationAssertion(Annotation( "GOC:curators") "The chemical reactions and pathways involving pyridine, a nitrogenous base (C5H5N) obtained from the distillation of bone oil or coal tar, and by the decomposition of certain alkaloids, as a colorless liquid with a peculiar pungent odor.") @@ -8649,7 +8611,6 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019507") AnnotationAssertion(rdfs:label "pyridine metabolic process") -SubClassOf( ) SubClassOf( ) # Class: (taurine metabolic process) @@ -8666,6 +8627,7 @@ SubClassOf( "GOC:ma") "The chemical reactions and pathways involving a protein. Includes protein modification.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "GO:0006411") AnnotationAssertion( "GO:0044267") AnnotationAssertion( "GO:0044268") @@ -8678,12 +8640,14 @@ AnnotationAssertion( "multicellular organismal protein metabolic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019538") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "protein metabolic process") SubClassOf( ) SubClassOf( ) @@ -8711,7 +8675,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organophosphate metabolic process") SubClassOf( ) -SubClassOf( ) # Class: (NAD metabolic process) @@ -8824,7 +8787,6 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019857") AnnotationAssertion(rdfs:label "5-methylcytosine metabolic process") -SubClassOf( ) SubClassOf( ) # Class: (cytosine metabolic process) @@ -8924,12 +8886,15 @@ SubClassOf( ObjectSomeValuesFrom( (cellular component disassembly) AnnotationAssertion(Annotation( "GOC:isa_complete") "A cellular process that results in the breakdown of a cellular component.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "GO:0071845") AnnotationAssertion( "cell structure disassembly") AnnotationAssertion( "cellular component disassembly at cellular level") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0022411") +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "cellular component disassembly") SubClassOf( ) DisjointClasses( ) @@ -9156,7 +9121,7 @@ SubClassOf( (cell projection organization) -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mah") Annotation( "http://www.cogsci.princeton.edu/~wn/") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.") +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mah") Annotation( "PMID:16318917") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26279"^^xsd:anyURI) AnnotationAssertion( "cell projection organisation") AnnotationAssertion( "biological_process") @@ -9169,7 +9134,7 @@ SubClassOf( (cell projection assembly) -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mah") Annotation( "http://www.cogsci.princeton.edu/~wn/") "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.") +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mah") Annotation( "PMID:18391171") "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.") AnnotationAssertion( "formation of a cell surface projection") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mah") "cell projection biogenesis") @@ -9806,10 +9771,12 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cellular metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "regulation of cellular metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0031323") AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of cellular metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -9819,6 +9786,7 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of cellular metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "down regulation of cellular metabolic process") AnnotationAssertion( "down-regulation of cellular metabolic process") AnnotationAssertion( "downregulation of cellular metabolic process") @@ -9827,6 +9795,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0031324") AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of cellular metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -9837,6 +9806,7 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cellular metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "positive regulation of cellular metabolism") AnnotationAssertion( "up regulation of cellular metabolic process") AnnotationAssertion( "up-regulation of cellular metabolic process") @@ -9846,6 +9816,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0031325") AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "positive regulation of cellular metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -9856,12 +9827,15 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cellular biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "regulation of cellular anabolism") AnnotationAssertion( "regulation of cellular biosynthesis") AnnotationAssertion( "regulation of cellular formation") AnnotationAssertion( "regulation of cellular synthesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0031326") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of cellular biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -9871,6 +9845,7 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of cellular biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "down regulation of cellular biosynthetic process") AnnotationAssertion( "down-regulation of cellular biosynthetic process") AnnotationAssertion( "downregulation of cellular biosynthetic process") @@ -9881,6 +9856,8 @@ AnnotationAssertion( "inhibition of cellular biosynthetic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0031327") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of cellular biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -9891,6 +9868,7 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cellular biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "positive regulation of cellular anabolism") AnnotationAssertion( "positive regulation of cellular biosynthesis") AnnotationAssertion( "positive regulation of cellular formation") @@ -9902,6 +9880,8 @@ AnnotationAssertion( "stimulation of cellular biosynthetic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0031328") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "positive regulation of cellular biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -10309,6 +10289,7 @@ SubClassOf( ObjectSomeValuesFrom( (multicellular organismal process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -10323,6 +10304,7 @@ AnnotationAssertion( "GO:0032501") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "multicellular organismal process") SubClassOf( ) @@ -10368,9 +10350,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study.") AnnotationAssertion(rdfs:label "RNA biosynthetic process") -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (monocarboxylic acid metabolic process) @@ -10419,7 +10399,7 @@ AnnotationAssertion( "GO:0032870") AnnotationAssertion(rdfs:label "cellular response to hormone stimulus") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (regulation of establishment or maintenance of cell polarity) @@ -10749,7 +10729,7 @@ AnnotationAssertion( "GO:0033238") AnnotationAssertion(rdfs:label "regulation of amine metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of amine metabolic process) @@ -10761,8 +10741,8 @@ AnnotationAssertion( "GO:0033239") AnnotationAssertion(rdfs:label "negative regulation of amine metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of amine metabolic process) @@ -10774,8 +10754,8 @@ AnnotationAssertion( "GO:0033240") AnnotationAssertion(rdfs:label "positive regulation of amine metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (protein localization to organelle) @@ -10918,7 +10898,7 @@ AnnotationAssertion( "GO:0034248") AnnotationAssertion(rdfs:label "regulation of amide metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of amide metabolic process) @@ -10930,8 +10910,8 @@ AnnotationAssertion( "GO:0034249") AnnotationAssertion(rdfs:label "negative regulation of amide metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of amide metabolic process) @@ -10943,8 +10923,8 @@ AnnotationAssertion( "GO:0034250") AnnotationAssertion(rdfs:label "positive regulation of amide metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of urea metabolic process) @@ -10970,19 +10950,6 @@ AnnotationAssertion( "primary alcohol metabolic process") SubClassOf( ) -# Class: (cellular nitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "cellular nitrogen compound metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0034641") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular nitrogen compound metabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (nucleobase-containing compound biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.") @@ -10994,9 +10961,7 @@ AnnotationAssertion( "GO:0034654") AnnotationAssertion(rdfs:label "nucleobase-containing compound biosynthetic process") SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: () @@ -11233,11 +11198,10 @@ SubClassOf( (intraciliary transport involved in cilium assembly) -AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:cilia") Annotation( "Reactome:R-HSA-5620924.2") "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.") +AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:cilia") "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.") AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T10:55:42Z") AnnotationAssertion( "intraflagellar transport") -AnnotationAssertion( "Reactome:R-HSA-5620924.2") AnnotationAssertion( "biological_process") AnnotationAssertion( "intraciliary transport involved in cilium morphogenesis") AnnotationAssertion( "intraflagellar transport involved in cilium morphogenesis") @@ -11525,7 +11489,7 @@ SubClassOf( ObjectSomeValuesFrom( (intraciliary transport) -AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:kmv") Annotation( "PMID:17981739") Annotation( "PMID:18180368") Annotation( "PMID:22869374") Annotation( "Reactome:R-HSA-5620924.2") "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins.") +AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:kmv") Annotation( "PMID:17981739") Annotation( "PMID:18180368") Annotation( "PMID:22869374") "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -11549,7 +11513,7 @@ SubClassOf( ObjectSomeValuesFrom( (cell migration involved in gastrulation) -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0878932437") Annotation( "http://www.cellmigration.org/") "The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression).") +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "PMID:16099638") "The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression).") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042074") AnnotationAssertion(rdfs:label "cell migration involved in gastrulation") @@ -11579,7 +11543,6 @@ AnnotationAssertion( "cellular ketone metabolic process") SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (response to chemical) @@ -11648,8 +11611,11 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of phosphorylation) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042325") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "regulation of phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -11658,12 +11624,15 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of phosphorylation) AnnotationAssertion(Annotation( "GOC:jl") "Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "down regulation of phosphorylation") AnnotationAssertion( "down-regulation of phosphorylation") AnnotationAssertion( "downregulation of phosphorylation") AnnotationAssertion( "inhibition of phosphorylation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042326") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "negative regulation of phosphorylation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -11722,10 +11691,6 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042430") AnnotationAssertion(rdfs:label "indole-containing compound metabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (ethanolamine-containing compound metabolic process) @@ -11800,8 +11765,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0042537") AnnotationAssertion(rdfs:label "benzene-containing compound metabolic process") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (homeostatic process) @@ -11859,6 +11823,7 @@ SubClassOf( (regulation of apoptotic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mtg_apoptosis") "Any process that modulates the occurrence or rate of cell death by apoptotic process.") +AnnotationAssertion( ) AnnotationAssertion( "regulation of apoptosis") AnnotationAssertion( "biological_process") AnnotationAssertion( "apoptosis regulator activity") @@ -11871,7 +11836,7 @@ SubClassOf( ObjectSomeValuesFrom( (cell projection) -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "http://www.cogsci.princeton.edu/~wn/") "A prolongation or process extending from a cell, e.g. a flagellum or axon.") +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "PMID:16318917") "A prolongation or process extending from a cell, e.g. a flagellum or axon.") AnnotationAssertion( "cell process") AnnotationAssertion( "cellular process") AnnotationAssertion( "cellular projection") @@ -11918,6 +11883,7 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of apoptotic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.") +AnnotationAssertion( ) AnnotationAssertion( "GO:0006916") AnnotationAssertion( "anti-apoptosis") AnnotationAssertion( "down regulation of apoptosis") @@ -12069,7 +12035,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "macromolecule metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (organelle) @@ -12555,13 +12521,16 @@ SubClassOf( ObjectSomeValuesFrom( (amide metabolic process) AnnotationAssertion(Annotation( "GOC:curators") "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "amide metabolism") AnnotationAssertion( "cellular amide metabolic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043603") +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "amide metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (amide biosynthetic process) @@ -12569,8 +12538,8 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0043604") AnnotationAssertion(rdfs:label "amide biosynthetic process") +SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (inositol phosphate metabolic process) @@ -12714,8 +12683,9 @@ SubClassOf( (primary metabolic process) -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "http://www.metacyc.org") "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.") +AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) +AnnotationAssertion( "Wikipedia:Primary_metabolite") AnnotationAssertion( "primary metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044238") @@ -12754,19 +12724,6 @@ AnnotationAssertion(rdfs:label "cell SubClassOf( ) SubClassOf( ) -# Class: (cellular nitrogen compound biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.") -AnnotationAssertion( "nitrogen compound anabolism") -AnnotationAssertion( "nitrogen compound biosynthesis") -AnnotationAssertion( "nitrogen compound formation") -AnnotationAssertion( "nitrogen compound synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044271") -AnnotationAssertion(rdfs:label "cellular nitrogen compound biosynthetic process") -SubClassOf( ) -SubClassOf( ) - # Class: (small molecule metabolic process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:pde") Annotation( "GOC:vw") "The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.") @@ -12782,6 +12739,19 @@ AnnotationAssertion(rdfs:comment "Sm AnnotationAssertion(rdfs:label "small molecule metabolic process") SubClassOf( ) +# Class: (small molecule catabolic process) + +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:vw") "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2010-01-26T12:06:10Z") +AnnotationAssertion( "small molecule catabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0044282") +AnnotationAssertion(rdfs:comment "Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.") +AnnotationAssertion(rdfs:label "small molecule catabolic process") +SubClassOf( ) +SubClassOf( ) + # Class: (small molecule biosynthetic process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:pde") Annotation( "GOC:vw") "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.") @@ -13620,9 +13590,8 @@ AnnotationAssertion(Annotation( "GO:0045934") AnnotationAssertion(rdfs:label "negative regulation of nucleobase-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of nucleobase-containing compound metabolic process) @@ -13639,9 +13608,8 @@ AnnotationAssertion(Annotation( "GO:0045935") AnnotationAssertion(rdfs:label "positive regulation of nucleobase-containing compound metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of phosphate metabolic process) @@ -14081,6 +14049,19 @@ SubClassOf( ) SubClassOf( ) +# Class: (monosaccharide catabolic process) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms.") +AnnotationAssertion( "monosaccharide breakdown") +AnnotationAssertion( "monosaccharide catabolism") +AnnotationAssertion( "monosaccharide degradation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0046365") +AnnotationAssertion(rdfs:label "monosaccharide catabolic process") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + # Class: (2-deoxyribose 1-phosphate metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving 2-deoxyribose 1-phosphate, the phosphorylated sugar 1-phospho-2-deoxyribose.") @@ -14125,18 +14106,6 @@ AnnotationAssertion( "creatinine metabolic process") SubClassOf( ) -# Class: (heterocycle metabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).") -AnnotationAssertion( "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( ) - # Class: (glycerolipid metabolic process) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "PMID:8906569") "The chemical reactions and pathways involving glycerolipids, any lipid with a glycerol backbone. Diacylglycerol and phosphatidate are key lipid intermediates of glycerolipid biosynthesis.") @@ -15098,6 +15067,7 @@ SubClassOf( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:mlg") "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19809"^^xsd:anyURI) +AnnotationAssertion( ) AnnotationAssertion( "cell locomotion") AnnotationAssertion( "movement of a cell") AnnotationAssertion( "biological_process") @@ -15327,6 +15297,7 @@ SubClassOf( (regulation of cell activation) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.") +AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050865") AnnotationAssertion(rdfs:label "regulation of cell activation") @@ -15685,53 +15656,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of nitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") -AnnotationAssertion(Annotation( "GOC:tb") "regulation of nitrogen metabolic process") -AnnotationAssertion( "regulation of nitrogen metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051171") -AnnotationAssertion(rdfs:label "regulation of nitrogen compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of nitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") -AnnotationAssertion( "down regulation of nitrogen metabolic process") -AnnotationAssertion( "down-regulation of nitrogen metabolic process") -AnnotationAssertion( "downregulation of nitrogen metabolic process") -AnnotationAssertion(Annotation( "GOC:tb") "negative regulation of nitrogen metabolic process") -AnnotationAssertion( "negative regulation of nitrogen metabolism") -AnnotationAssertion( "inhibition of nitrogen metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051172") -AnnotationAssertion(rdfs:label "negative regulation of nitrogen compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of nitrogen compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:tb") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.") -AnnotationAssertion(Annotation( "GOC:tb") "positive regulation of nitrogen metabolic process") -AnnotationAssertion( "positive regulation of nitrogen metabolism") -AnnotationAssertion( "up regulation of nitrogen metabolic process") -AnnotationAssertion( "up-regulation of nitrogen metabolic process") -AnnotationAssertion( "upregulation of nitrogen metabolic process") -AnnotationAssertion( "activation of nitrogen metabolic process") -AnnotationAssertion( "stimulation of nitrogen metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0051173") -AnnotationAssertion(rdfs:label "positive regulation of nitrogen compound metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (regulation of phosphorus metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.") @@ -15900,7 +15824,6 @@ AnnotationAssertion( "GO:0051246") AnnotationAssertion(rdfs:label "regulation of protein metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -15928,7 +15851,6 @@ AnnotationAssertion( "positive regulation of protein metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -15953,7 +15875,6 @@ AnnotationAssertion( "negative regulation of protein metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -16452,6 +16373,7 @@ SubClassOf( (cellular localization) AnnotationAssertion(Annotation( "GOC:tb") Annotation( "GOC:vw") "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-18T14:04:32Z") AnnotationAssertion( "GO:1902580") @@ -16464,7 +16386,9 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism cellular localization") AnnotationAssertion( "GO:0051641") +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "cellular localization") SubClassOf( ) SubClassOf( ) @@ -16482,7 +16406,7 @@ SubClassOf( (establishment of localization in cell) -AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dos") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.") +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dos") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.") AnnotationAssertion(Annotation( "GOC:mah") "establishment of localisation in cell") AnnotationAssertion( "establishment of intracellular localization") AnnotationAssertion( "establishment of localization within cell") @@ -16983,6 +16907,15 @@ AnnotationAssertion( "histamine oxidase activity") SubClassOf( ) +# Class: (imidazole-containing compound metabolic process) + +AnnotationAssertion(Annotation( "GOC:curators") "The chemical reactions and pathways involving imidazoles, five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton.") +AnnotationAssertion( "imidazole metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0052803") +AnnotationAssertion(rdfs:label "imidazole-containing compound metabolic process") +SubClassOf( ) + # Class: (muscle cell development) AnnotationAssertion(Annotation( "CL:0000187") Annotation( "GOC:devbiol") "The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate.") @@ -17126,7 +17059,7 @@ SubClassOf( ObjectSomeValuesFrom( (oviduct development) -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:ebc") Annotation( "http://www.thefreedictionary.com/oviduct") "The reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:ebc") Annotation( "PMID:22918811") Annotation( "PMID:27875265") "The reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism.") AnnotationAssertion(Annotation( "GOC:bf") "fallopian tube development") AnnotationAssertion( "biological_process") AnnotationAssertion( "Mullerian tract development") @@ -17225,7 +17158,7 @@ SubClassOf( ObjectSomeValuesFrom( (cilium assembly) -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:cilia") Annotation( "GOC:dph") Annotation( "GOC:kmv") Annotation( "GOC:pr") Annotation( "GOC:vw") Annotation( "ISBN:0198506732") Annotation( "PMID:13978319") Annotation( "PMID:27350441") Annotation( "Reactome:R-HSA-5617833.2") "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.") +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:cilia") Annotation( "GOC:dph") Annotation( "GOC:kmv") Annotation( "GOC:pr") Annotation( "GOC:vw") Annotation( "ISBN:0198506732") Annotation( "PMID:13978319") Annotation( "PMID:27350441") "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -17233,7 +17166,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "GO:0042384") -AnnotationAssertion( "Reactome:R-HSA-5617833.2") AnnotationAssertion( "ciliogenesis") AnnotationAssertion( "cilium formation") AnnotationAssertion( "microtubule-based flagellum assembly") @@ -17978,17 +17910,20 @@ AnnotationAssertion( "axon development") SubClassOf( ) -# Class: (mannose to fructose-6-phosphate metabolic process) +# Class: (mannose to fructose-6-phosphate catabolic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "ISBN:0201090910") Annotation( "ISBN:0879010479") "The chemical reactions and pathways in which mannose, the aldohexose manno-hexose, is converted to fructose-6-phosphate.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27638"^^xsd:anyURI) AnnotationAssertion( "dph") AnnotationAssertion( "2014-04-03T13:38:50Z") +AnnotationAssertion( "MetaCyc:MANNCAT-PWY") +AnnotationAssertion( "MetaCyc:PWY3O-1743") AnnotationAssertion(Annotation( "GOC:dph") "mannose metabolism to fructose-6-phosphate") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061611") -AnnotationAssertion(rdfs:label "mannose to fructose-6-phosphate metabolic process") +AnnotationAssertion(rdfs:label "mannose to fructose-6-phosphate catabolic process") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (cytoskeleton-dependent cytokinesis) @@ -18337,17 +18272,6 @@ AnnotationAssertion(rdfs:label "cell SubClassOf( ) SubClassOf( ) -# Class: (cellular response to organic substance) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2009-12-10T04:46:04Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0071310") -AnnotationAssertion(rdfs:label "cellular response to organic substance") -SubClassOf( ) -SubClassOf( ) - # Class: (cellular response to growth factor stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.") @@ -18383,7 +18307,6 @@ AnnotationAssertion( "GO:0071417") AnnotationAssertion(rdfs:label "cellular response to organonitrogen compound") SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -18448,31 +18371,6 @@ AnnotationAssertion( "organism emergence from protective structure") SubClassOf( ) -# Class: (organic substance transport) - -AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.") -AnnotationAssertion( "mah") -AnnotationAssertion( "2010-03-08T02:15:14Z") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0071702") -AnnotationAssertion(rdfs:label "organic substance transport") -SubClassOf( ) - -# Class: (organic substance metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) -AnnotationAssertion( "mah") -AnnotationAssertion( "2010-03-08T03:32:18Z") -AnnotationAssertion( "organic molecular entity metabolic process") -AnnotationAssertion( "organic molecular entity metabolism") -AnnotationAssertion( "organic substance metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0071704") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organic substance metabolic process") -SubClassOf( ) - # Class: (nitrogen compound transport) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") @@ -18536,6 +18434,7 @@ SubClassOf( (cellular component organization or biogenesis) AnnotationAssertion(Annotation( "GOC:mah") "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-10T01:39:16Z") AnnotationAssertion( "GO:0071841") @@ -18544,8 +18443,10 @@ AnnotationAssertion(Annotation( "cellular component organization or biogenesis at cellular level") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071840") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "cellular component organization or biogenesis") SubClassOf( ) @@ -18614,7 +18515,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "nitrogen cycle metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (cell periphery) @@ -18666,8 +18567,6 @@ AnnotationAssertion( "lactam metabolic process") SubClassOf( ) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (sulfur compound transport) @@ -18715,10 +18614,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0072521") AnnotationAssertion(rdfs:label "purine-containing compound metabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (pyridine-containing compound metabolic process) @@ -18731,9 +18626,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0072524") AnnotationAssertion(rdfs:label "pyridine-containing compound metabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (pyrimidine-containing compound metabolic process) @@ -18746,9 +18638,6 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:0072527") AnnotationAssertion(rdfs:label "pyrimidine-containing compound metabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (regulation of primary metabolic process) @@ -19130,7 +19019,7 @@ SubClassOf( ObjectSomeValuesFrom( (cell migration involved in somitogenic axis elongation) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process involved in the controlled self-propelled movement of a cell that contributes to somitogenic axis elongation.") -AnnotationAssertion( "https://github.com/geneontology/go-annotation/issues/2040"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15967"^^xsd:anyURI) AnnotationAssertion( "tb") AnnotationAssertion( "2010-01-22T11:13:59Z") AnnotationAssertion( "GO:0090247") @@ -19145,7 +19034,7 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cell migration involved in somitogenic axis elongation) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate, or extent of the controlled self-propelled movement of a cell that contributes to somitogenic axis elongation.") -AnnotationAssertion( "https://github.com/geneontology/go-annotation/issues/2040"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15967"^^xsd:anyURI) AnnotationAssertion( "tb") AnnotationAssertion( "2010-01-22T11:20:05Z") AnnotationAssertion( "regulation of cell motility involved in somitogenic axis elongation") @@ -19490,7 +19379,7 @@ SubClassOf( (vesicle targeting, trans-Golgi to periciliary membrane compartment) -AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:20106869") Annotation( "PMID:23351793") Annotation( "PMID:24814148") Annotation( "PMID:26485645") Annotation( "Reactome:R-HSA-5620920.1") "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces.") +AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:20106869") Annotation( "PMID:23351793") Annotation( "PMID:24814148") Annotation( "PMID:26485645") "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces.") AnnotationAssertion( "pr") AnnotationAssertion( "2016-08-05T16:16:28Z") AnnotationAssertion( "biological_process") @@ -19847,7 +19736,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120254") AnnotationAssertion(rdfs:label "olefinic compound metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (regulation of pigmentation) @@ -20079,6 +19968,7 @@ SubClassOf( "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( "https://github.com/geneontology/go-ontology/issues/27633"^^xsd:anyURI) AnnotationAssertion( "pg") AnnotationAssertion( "2024-03-25T07:33:40Z") AnnotationAssertion( "biological_process") @@ -20086,6 +19976,8 @@ 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( ) +SubClassOf( ) SubClassOf( ) # Class: (L-amino acid metabolic process) @@ -20357,7 +20249,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "carbohydrate derivative metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (primary amino compound metabolic process) @@ -20476,32 +20368,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (organic cyclic compound metabolic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways involving organic cyclic compound.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2012-09-14T09:03:51Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic cyclic compound metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901360") -AnnotationAssertion(rdfs:label "organic cyclic compound metabolic process") -SubClassOf( ) - -# Class: (organic cyclic compound biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the formation of organic cyclic compound.") -AnnotationAssertion( "bf") -AnnotationAssertion( "2012-09-14T09:05:22Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic cyclic compound anabolism") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic cyclic compound biosynthesis") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic cyclic compound formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic cyclic compound synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901362") -AnnotationAssertion(rdfs:label "organic cyclic compound biosynthetic process") -SubClassOf( ) -SubClassOf( ) - # Class: (organonitrogen compound metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways involving organonitrogen compound.") @@ -20513,8 +20379,7 @@ AnnotationAssertion( "GO:1901564") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organonitrogen compound metabolic process") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (organonitrogen compound biosynthetic process) @@ -20530,47 +20395,8 @@ AnnotationAssertion( "GO:1901566") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organonitrogen compound biosynthetic process") +SubClassOf( ) SubClassOf( ) -SubClassOf( ) - -# Class: (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( "organic molecular entity catabolic process") -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( ) - -# Class: (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") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity biosynthesis") -AnnotationAssertion( "organic molecular entity biosynthetic process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity formation") -AnnotationAssertion(Annotation( "GOC:TermGenie") "organic molecular entity synthesis") -AnnotationAssertion( "organic substance anabolism") -AnnotationAssertion( "organic substance biosynthesis") -AnnotationAssertion( "organic substance formation") -AnnotationAssertion( "organic substance synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:1901576") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organic substance biosynthetic process") -SubClassOf( ) -SubClassOf( ) # Class: (alpha-amino acid metabolic process) @@ -20594,7 +20420,7 @@ AnnotationAssertion(Annotation( "biological_process") AnnotationAssertion( "GO:1901615") AnnotationAssertion(rdfs:label "organic hydroxy compound metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (glycosyl compound metabolic process) @@ -20638,22 +20464,28 @@ SubClassOf( ObjectSomeValuesFrom( (response to nitrogen compound) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:06:08Z") AnnotationAssertion( "response to nitrogen molecular entity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901698") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "response to nitrogen compound") SubClassOf( ) # Class: (cellular response to nitrogen compound) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:06:13Z") AnnotationAssertion( "cellular response to nitrogen molecular entity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901699") +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 nitrogen compound") SubClassOf( ) SubClassOf( ) @@ -20661,11 +20493,14 @@ SubClassOf( (response to oxygen-containing compound) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:11:37Z") AnnotationAssertion( "response to oxygen molecular entity") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901700") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "response to oxygen-containing compound") SubClassOf( ) @@ -21869,7 +21704,7 @@ AnnotationAssertion( "GO:1903314") AnnotationAssertion(rdfs:label "regulation of nitrogen cycle metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of nitrogen cycle metabolic process) @@ -21885,7 +21720,7 @@ AnnotationAssertion( "GO:1903315") AnnotationAssertion(rdfs:label "negative regulation of nitrogen cycle metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21902,7 +21737,7 @@ AnnotationAssertion( "GO:1903316") AnnotationAssertion(rdfs:label "positive regulation of nitrogen cycle metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -24092,7 +23927,6 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of thyroid hormone generation) @@ -24106,7 +23940,6 @@ AnnotationAssertion(rdfs:label "nega EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -24121,7 +23954,6 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 3d35884..f0f7155 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-18") +Annotation(owl:versionInfo "2024-08-18") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/nbo_import.owl b/src/ontology/imports/nbo_import.owl index cb7f9ad..d7d4599 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 "2024-04-18") +Annotation(owl:versionInfo "2024-08-18") Declaration(Class()) Declaration(Class()) @@ -136,7 +136,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -174,7 +173,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -310,7 +308,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -2533,12 +2530,6 @@ SubClassOf( ObjectAllValuesFrom( "morphology") SubClassOf( ) -# Class: (shape) - -AnnotationAssertion(rdfs:comment "Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.") -AnnotationAssertion(rdfs:label "shape") -SubClassOf( ) - # Class: (qualitative) AnnotationAssertion(rdfs:comment "TODO: define this or obsolete it and move children somewhere else.") @@ -2797,14 +2788,6 @@ EquivalentClasses( ObjectIntersecti SubClassOf( ) SubClassOf( ) -# Class: (anatomical entity) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anatomical entity") -SubClassOf( ) - SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) SubObjectPropertyOf(ObjectPropertyChain( ) ) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 4057f55..88108da 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 "2024-04-18") +Annotation(owl:versionInfo "2024-08-18") Declaration(Class()) Declaration(Class()) @@ -3987,7 +3987,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5974,7 +5973,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -6406,10 +6404,6 @@ AnnotationAssertion(rdfs:label "has_narrow_synonym") -# Annotation Property: (id) - -AnnotationAssertion(rdfs:label "id") - # Annotation Property: rdfs:seeAlso (see also) AnnotationAssertion( rdfs:seeAlso "http://www.w3.org/2000/01/rdf-schema#seeAlso") @@ -66724,17 +66718,6 @@ AnnotationAssertion( "mislocalised medially") SubClassOf( ) -# Class: (blistered) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A texture quality inhering in a bearer by virtue of a local accumulation of fluid underneath the surface of the bearer.") -AnnotationAssertion( "blistering") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0001928") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "blistered") -SubClassOf( ) - # Class: (variability of size) AnnotationAssertion(Annotation( "PATOC:GVG") "A variability quality inhering in a bearer by virtue of whether the bearer exhibits size variation or change.") diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index bba121b..b965769 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 "2024-04-18") + +Annotation( ) +Annotation(owl:versionInfo "2024-08-18") Declaration(Class()) Declaration(Class()) @@ -119,7 +119,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -145,7 +144,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -354,7 +352,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "part of"@en) -AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) @@ -381,7 +378,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part"@en) -AnnotationAssertion(rdfs:label "has part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -425,11 +421,9 @@ AnnotationAssertion( "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) -AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (contains process) @@ -465,8 +459,6 @@ AnnotationAssertion( "is bearer of"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has characteristic"@en) -AnnotationAssertion(rdfs:label "has characteristic") -AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -494,9 +486,7 @@ AnnotationAssertion( "has_participant"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) -AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (function of) @@ -963,7 +953,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) -AnnotationAssertion(rdfs:label "enabled by") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1326,17 +1315,6 @@ AnnotationAssertion( "molecular interaction relation helper property") SubObjectPropertyOf( ) -# Object Property: (results in movement of) - -AnnotationAssertion( "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c") -AnnotationAssertion( ) -AnnotationAssertion( "") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "results in movement of") -SubObjectPropertyOf( ) - # Object Property: (causally influences) AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") @@ -1552,10 +1530,10 @@ SubObjectPropertyOf( "A diagnostic testing device utilizes a specimen.") AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) @@ -1583,14 +1561,6 @@ AnnotationAssertion( "negatively regulates characteristic") SubObjectPropertyOf( ) -# Object Property: (results in changes to anatomical or cellular structure) - -AnnotationAssertion( "p has anatomical participant c iff p has participant c, and c is an anatomical entity") -AnnotationAssertion( ) -AnnotationAssertion( "2018-09-26T01:08:58Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "results in changes to anatomical or cellular structure") -SubObjectPropertyOf( ) - ############################ @@ -1627,7 +1597,6 @@ AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) # Class: (disposition) @@ -1660,7 +1629,6 @@ AnnotationAssertion(rdfs:seeAlso "h AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) # Class: (role) @@ -1743,7 +1711,6 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "biological process"@en) AnnotationAssertion(rdfs:label "biological_process") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (kinase activity) @@ -1997,17 +1964,17 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/xao_import.owl b/src/ontology/imports/xao_import.owl index 8ed61cf..bc9c67f 100644 --- a/src/ontology/imports/xao_import.owl +++ b/src/ontology/imports/xao_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-18") +Annotation(owl:versionInfo "2024-08-18") Declaration(Class()) Declaration(Class()) @@ -1734,7 +1734,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty())