From a799b4cf6b92b0bf21e504a9de00477ba1e34f36 Mon Sep 17 00:00:00 2001 From: sbello Date: Tue, 12 Nov 2024 19:03:32 +0000 Subject: [PATCH] Update imports and components --- src/ontology/imports/chebi_import.owl | 4 +- src/ontology/imports/cl_import.owl | 4 +- src/ontology/imports/go_import.owl | 1945 +++++++++++++++++------- src/ontology/imports/mpath_import.owl | 4 +- src/ontology/imports/nbo_import.owl | 4 +- src/ontology/imports/pato_import.owl | 4 +- src/ontology/imports/pr_import.owl | 118 +- src/ontology/imports/ro_import.owl | 4 +- src/ontology/imports/uberon_import.owl | 4 +- src/patterns/definitions.owl | 4 +- 10 files changed, 1497 insertions(+), 598 deletions(-) diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl index 4a2cb714..4df58961 100644 --- a/src/ontology/imports/chebi_import.owl +++ b/src/ontology/imports/chebi_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-11-11") +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl index 5fc02a3f..5a71366c 100644 --- a/src/ontology/imports/cl_import.owl +++ b/src/ontology/imports/cl_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-11-11") +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index efe3a86f..f00bbf7c 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 "2024-11-11") + +Annotation( ) +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class()) @@ -78,6 +78,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -630,9 +631,13 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -683,6 +688,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -885,7 +891,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1138,6 +1143,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1240,12 +1246,15 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1350,6 +1359,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1374,6 +1384,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1497,15 +1508,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1558,8 +1560,13 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1678,6 +1685,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1712,9 +1720,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1752,6 +1757,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2006,6 +2012,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2070,6 +2079,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2096,13 +2107,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2291,6 +2298,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2315,8 +2324,12 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2399,7 +2412,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2962,8 +2974,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3149,10 +3163,15 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3207,6 +3226,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3253,6 +3273,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3417,6 +3438,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3438,6 +3462,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3577,6 +3603,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3593,6 +3623,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3652,6 +3685,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3692,6 +3728,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3981,6 +4020,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4018,6 +4060,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4110,6 +4153,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4211,6 +4257,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4333,6 +4381,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4349,7 +4400,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -4657,6 +4707,7 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (citrulline metabolic process) @@ -4938,7 +4989,6 @@ SubClassOf( (synaptonemal complex) AnnotationAssertion(Annotation( "DOI:10.5772/29752") Annotation( "GOC:elh") "A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.") -AnnotationAssertion( ) AnnotationAssertion( "GO:0005716") AnnotationAssertion( "Wikipedia:Synaptonemal_complex") AnnotationAssertion( "cellular_component") @@ -5065,7 +5115,6 @@ SubClassOf( (action potential) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:go_curators") Annotation( "GOC:tb") Annotation( "ISBN:978-0-07-139011-8") "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0001508") AnnotationAssertion(rdfs:comment "Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so.") @@ -5105,7 +5154,6 @@ SubClassOf( ObjectSomeValuesFrom( (cornified envelope) AnnotationAssertion(Annotation( "GOC:add") Annotation( "PMID:11112355") Annotation( "PMID:11590230") Annotation( "PMID:15803139") "A type of plasma membrane that has been modified through addition of distinct intracellular and extracellular components, including ceramide, found in cornifying epithelial cells (corneocytes).") -AnnotationAssertion( ) AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0001533") AnnotationAssertion(rdfs:label "cornified envelope") @@ -5449,6 +5497,16 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (formation of translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:hjd") "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).") +AnnotationAssertion( "translation initiation ternary complex assembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0001677") +AnnotationAssertion(rdfs:label "formation of translation initiation ternary complex") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (in utero embryonic development) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:mtg_sensu") "The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.") @@ -5817,8 +5875,6 @@ SubClassOf( (regulation of cytokine production) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") "Any process that modulates the frequency, rate, or extent of production of a cytokine.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "GO:0042035") AnnotationAssertion( "GO:0050707") AnnotationAssertion( "regulation of cytokine anabolism") @@ -7238,7 +7294,6 @@ SubClassOf( ObjectSomeValuesFrom( (immune system process) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GO_REF:0000022") "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.") -AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Immune_system") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002376") @@ -10834,12 +10889,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:dph") Annotation( "GOC:jl") "The directed, self-propelled movement of a cilium.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19809"^^xsd:anyURI) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-24T09:56:26Z") AnnotationAssertion( "GO:0036142") @@ -11063,7 +11112,7 @@ SubClassOf( (alkaline phosphatase activity) -AnnotationAssertion(Annotation( "EC:3.1.3.1") Annotation( "RHEA:15017") "Catalysis of the reaction: a phosphate monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.") +AnnotationAssertion(Annotation( "EC:3.1.3.1") "Catalysis of the reaction: a phosphate monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.") AnnotationAssertion(Annotation( "EC:3.1.3.1") "glycerophosphatase activity") AnnotationAssertion(Annotation( "EC:3.1.3.1") "phosphomonoesterase activity") AnnotationAssertion( "EC:3.1.3.1") @@ -11325,7 +11374,6 @@ AnnotationAssertion(Annotation(rdfs:label "CYP4F8 19-hydroxylates PGH2") "Reactome:R-HSA-211924") AnnotationAssertion(Annotation(rdfs:label "CYP2C19 5-hydroxylates omeprazole") "Reactome:R-HSA-211929") AnnotationAssertion(Annotation(rdfs:label "CYP3A4 can N-demethylate loperamide") "Reactome:R-HSA-211948") -AnnotationAssertion(Annotation(rdfs:label "CYP1B1 4-hydroxylates EST17b") "Reactome:R-HSA-211951") AnnotationAssertion(Annotation(rdfs:label "CYP3A43 6b-hydroxylates TEST") "Reactome:R-HSA-211959") AnnotationAssertion(Annotation(rdfs:label "CYP2U1 19-hydroxylates ARA") "Reactome:R-HSA-211960") AnnotationAssertion(Annotation(rdfs:label "CYP4F11 16-hydroxylates 3OH-PALM") "Reactome:R-HSA-211962") @@ -11336,12 +11384,12 @@ AnnotationAssertion(Annotation(rdfs:label "CYP2C18 initiates bioactivation of ph AnnotationAssertion(Annotation(rdfs:label "CYP2F1 dehydrogenates 3-methylindole") "Reactome:R-HSA-212005") AnnotationAssertion(Annotation(rdfs:label "CYP3A4,5 oxidise AFB1 to AFXBO") "Reactome:R-HSA-213175") AnnotationAssertion(Annotation(rdfs:label "CYP4F3 20-hydroxylates LTB4") "Reactome:R-HSA-215526") -AnnotationAssertion(Annotation(rdfs:label "Arachidonic acid is hydroxylated to 16/17/18-HETE by CYP(1)") "Reactome:R-HSA-2161795") -AnnotationAssertion(Annotation(rdfs:label "Arachidonic acid is hydroxylated to 19-HETE by CYP(2)") "Reactome:R-HSA-2161814") -AnnotationAssertion(Annotation(rdfs:label "Arachidonic acid is epoxidated to 5,6-EET by CYP(4)") "Reactome:R-HSA-2161890") -AnnotationAssertion(Annotation(rdfs:label "Arachidonic acid is epoxidated to 8,9/11,12/14,15-EET by CYP(5)") "Reactome:R-HSA-2161899") -AnnotationAssertion(Annotation(rdfs:label "Arachidonic acid is hydroxylated to 20-HETE by CYP(3)") "Reactome:R-HSA-2161940") -AnnotationAssertion(Annotation(rdfs:label "DMPhOH is hydroxylated to MDMQ10H2 by DMPhOH monooxygenase") "Reactome:R-HSA-2162191") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is hydroxylated to 16-HETE by CYP(1)") "Reactome:R-HSA-2161795") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is hydroxylated to 19-HETE by CYP(2)") "Reactome:R-HSA-2161814") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is epoxidated to 5,6-EET by CYP(4)") "Reactome:R-HSA-2161890") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is epoxidated to 8,9-EET by CYP(5)") "Reactome:R-HSA-2161899") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is hydroxylated to 20-HETE by CYP(3)") "Reactome:R-HSA-2161940") +AnnotationAssertion(Annotation(rdfs:label "Unknown enzyme hydroxylates DMPhOH") "Reactome:R-HSA-2162191") AnnotationAssertion(Annotation(rdfs:label "FMO2:FAD:Mg2+ S-oxidises MTZ") "Reactome:R-HSA-217258") AnnotationAssertion(Annotation(rdfs:label "CYP2A13 oxidises AFM1 to AFM1E") "Reactome:R-HSA-5423647") AnnotationAssertion(Annotation(rdfs:label "CYP3A4,5 hydroxylates AFB1 to AFQ1") "Reactome:R-HSA-5423664") @@ -11354,7 +11402,6 @@ AnnotationAssertion(Annotation(rdfs:label "Defective CYP1B1 does not 4-hydroxyla AnnotationAssertion(Annotation(rdfs:label "Tyrosinase oxidises tyrosine to dopaquinone") "Reactome:R-HSA-5662662") AnnotationAssertion(Annotation(rdfs:label "Dopa is oxidized to dopaquinone by TYR") "Reactome:R-HSA-5662692") AnnotationAssertion(Annotation(rdfs:label "DHI and DHICA polymerize forming eumelanin") "Reactome:R-HSA-5663050") -AnnotationAssertion(Annotation(rdfs:label "CYP4V2 omega-hydroxylates DHA to HDoHE") "Reactome:R-HSA-6786239") AnnotationAssertion(Annotation(rdfs:label "Vinyl chloride is oxidized to 2-Chloroethylene oxide") "Reactome:R-HSA-76354") AnnotationAssertion(Annotation(rdfs:label "N-hydroxylation of 4-aminobiphenyl") "Reactome:R-HSA-76373") AnnotationAssertion(Annotation(rdfs:label "CYP1A2 S-demethylates 6MMP") "Reactome:R-HSA-76386") @@ -11381,6 +11428,10 @@ AnnotationAssertion(Annotation(rdfs:label "CYP3A4 monooxygenates ATVL to 2-OH-AT AnnotationAssertion(Annotation(rdfs:label "CYP3A4 monooxygenates ATV to 4-OH-ATV") "Reactome:R-HSA-9756162") AnnotationAssertion(Annotation(rdfs:label "CYP3A4 monooxygenates ATV to 2-OH-ATV") "Reactome:R-HSA-9756169") AnnotationAssertion(Annotation(rdfs:label "CYP3A4 monooxygenates ATVL to 4-OH-ATVL") "Reactome:R-HSA-9756180") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is epoxidated to 11,12-EET by CYP(5)") "Reactome:R-HSA-9915971") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is hydroxylated to 17-HETE by CYP(1)") "Reactome:R-HSA-9915992") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is hydroxylated to 18-HETE by CYP(1)") "Reactome:R-HSA-9915993") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is epoxidated to 14,15-EET by CYP(5)") "Reactome:R-HSA-9915997") AnnotationAssertion( "molecular_function") AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:vk") "hydroxylase activity") AnnotationAssertion( "GO:0004497") @@ -11666,7 +11717,7 @@ AnnotationAssertion(Annotation( "EC:2.7.1.40") AnnotationAssertion( "MetaCyc:PEPDEPHOS-RXN") AnnotationAssertion( "RHEA:18159") -AnnotationAssertion(Annotation(rdfs:label "phosphoenolpyruvate + ADP => pyruvate + ATP") "Reactome:R-HSA-71670") +AnnotationAssertion(Annotation(rdfs:label "PKM dephosphorylates PEP to PYR") "Reactome:R-HSA-71670") AnnotationAssertion( "molecular_function") AnnotationAssertion(Annotation( "EC:2.7.1.40") "ATP:pyruvate 2-O-phosphotransferase activity") AnnotationAssertion(Annotation( "EC:2.7.1.40") "phosphoenol transphosphorylase activity") @@ -11682,7 +11733,6 @@ AnnotationAssertion(Annotation( "https://github.com/geneontology/go-ontology/issues/28176"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28339"^^xsd:anyURI) AnnotationAssertion( "EC:3.1.1.3") -AnnotationAssertion( "EC:3.1.1.79") AnnotationAssertion( "MetaCyc:RXN-19278") AnnotationAssertion( "RHEA:12044") AnnotationAssertion(Annotation(rdfs:label "TAG is hydrolyzed to DAG by PNPLA2/3") "Reactome:R-HSA-1482777") @@ -11775,8 +11825,9 @@ SubClassOf( (calcium-activated cation channel activity) -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_transport") "Enables the calcium concentration-regulatable energy-independent passage of cations across a lipid bilayer down a concentration gradient.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_transport") "Enables the transmembrane transfer of an inorganic cation by a channel that opens when a calcium cation has been bound by the channel complex or one of its constituent parts.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24605"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28979"^^xsd:anyURI) AnnotationAssertion(Annotation(rdfs:label "TRPM4 transports Na+ from the extracellular region to the cytosol") "Reactome:R-HSA-9717383") AnnotationAssertion( "calcium activated cation channel activity") AnnotationAssertion( "intracellular calcium-activated potassium channel") @@ -11815,6 +11866,7 @@ SubClassOf( (potassium channel activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_transport") Annotation( "GOC:pr") Annotation( "ISBN:0815340729") "Enables the energy-independent facilitated diffusion of a potassium ion through a transmembrane aqueous pore or channel.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27521"^^xsd:anyURI) AnnotationAssertion(Annotation(rdfs:label "Activation of ATP sensitive Potassium channels in neuroendocrine cells") "Reactome:R-HSA-1296024") AnnotationAssertion(Annotation(rdfs:label "Activation of Ca2+ activated Potassium channels with Intermediate conductance") "Reactome:R-HSA-1296035") AnnotationAssertion(Annotation(rdfs:label "Activation of Ca2+ activated Potassium channels with large conductance") "Reactome:R-HSA-1296037") @@ -11879,6 +11931,7 @@ SubClassOf( "GOC:go_curators") "Binding to a protein.") AnnotationAssertion( "GO:0001948") AnnotationAssertion( "GO:0045308") +AnnotationAssertion(Annotation(rdfs:label "Intermediate II binds CYC1, UQCRC1, UQCRC2, UQCRH") "Reactome:R-HSA-9866132") AnnotationAssertion( "protein amino acid binding") AnnotationAssertion( "glycoprotein binding") AnnotationAssertion( "molecular_function") @@ -12243,7 +12296,6 @@ SubClassOf( ObjectSomeValuesFrom( (lysosome) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0198506732") "A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.") -AnnotationAssertion( ) AnnotationAssertion( "NIF_Subcellular:sao585356902") AnnotationAssertion( "Wikipedia:Lysosome") AnnotationAssertion( "cellular_component") @@ -12402,9 +12454,6 @@ SubClassOf( (centrosome) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0198547684") "A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Centrosome") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0005813") @@ -12644,7 +12693,6 @@ SubClassOf( (microvillus) AnnotationAssertion(Annotation( "ISBN:0815316194") "Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.") -AnnotationAssertion( ) AnnotationAssertion( "NIF_Subcellular:sao671419673") AnnotationAssertion( "Wikipedia:Microvillus") AnnotationAssertion( "cellular_component") @@ -12684,12 +12732,6 @@ SubClassOf( ObjectSomeValuesFrom( (cilium) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:curators") Annotation( "GOC:kmv") Annotation( "GOC:vw") Annotation( "ISBN:0198547684") Annotation( "PMID:16824949") Annotation( "PMID:17009929") Annotation( "PMID:20144998") "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "GO:0072372") AnnotationAssertion( "FMA:67181") AnnotationAssertion( "NIF_Subcellular:sao787716553") @@ -12878,7 +12920,6 @@ AnnotationAssertion( "GO:0006082") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "organic acid metabolic process") -SubClassOf( ) SubClassOf( ) # Class: (pyruvate metabolic process) @@ -12917,12 +12958,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "generation of precursor metabolites and energy") -SubClassOf( ) +SubClassOf( ) # Class: (gluconeogenesis) AnnotationAssertion(Annotation( "MetaCyc:GLUCONEO-PWY") "The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.") -AnnotationAssertion( "MetaCyc:GLUCONEO-PWY") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28953"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Gluconeogenesis") AnnotationAssertion( "glucose biosynthesis") AnnotationAssertion( "glucose biosynthetic process") @@ -12957,6 +12998,7 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (tricarboxylic acid cycle) @@ -13454,7 +13496,26 @@ AnnotationAssertion(rdfs:label "tran SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translational initiation) + +AnnotationAssertion(Annotation( "ISBN:019879276X") "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.") +AnnotationAssertion( "GO:0006440") +AnnotationAssertion( "GO:0006454") +AnnotationAssertion( "biopolymerisation") +AnnotationAssertion( "biopolymerization") +AnnotationAssertion( "protein synthesis initiation") +AnnotationAssertion( "translation initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006413") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "translational initiation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (translational elongation) @@ -13470,6 +13531,20 @@ AnnotationAssertion(rdfs:label "tran SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (translational termination) + +AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "ISBN:019879276X") "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).") +AnnotationAssertion( "GO:0006443") +AnnotationAssertion( "GO:0006456") +AnnotationAssertion( "protein synthesis termination") +AnnotationAssertion( "translation termination") +AnnotationAssertion( "translational complex disassembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006415") +AnnotationAssertion(rdfs:label "translational termination") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of translation) AnnotationAssertion(Annotation( "GOC:isa_complete") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.") @@ -13487,6 +13562,16 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of translational initiation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of translational initiation.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006446") +AnnotationAssertion(rdfs:label "regulation of translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of translational elongation) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate, extent or accuracy of translational elongation.") @@ -13497,6 +13582,17 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of translational termination) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of translational termination.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006449") +AnnotationAssertion(rdfs:label "regulation of translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (peptide metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.") @@ -13529,16 +13625,15 @@ AnnotationAssertion( "amino acid metabolic process") SubClassOf( ) -# Class: (regulation of cellular amino acid metabolic process) +# Class: (regulation of amino acid metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "regulation of amino acid metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006521") -AnnotationAssertion(rdfs:label "regulation of cellular amino acid metabolic process") +AnnotationAssertion(rdfs:label "regulation of amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -13591,13 +13686,14 @@ SubClassOf( (fatty acid metabolic process) AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Fatty_acid_metabolism") AnnotationAssertion( "fatty acid metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006631") AnnotationAssertion(rdfs:label "fatty acid metabolic process") +SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (fatty acid beta-oxidation) @@ -13608,26 +13704,30 @@ AnnotationAssertion( "fatty acid beta-oxidation") SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (membrane lipid metabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways involving membrane lipids, any lipid found in or associated with a biological membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "membrane lipid metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006643") AnnotationAssertion(rdfs:label "membrane lipid metabolic process") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (phospholipid metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "phospholipid metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006644") AnnotationAssertion(rdfs:label "phospholipid metabolic process") +SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (sphingolipid metabolic process) @@ -13665,6 +13765,7 @@ SubClassOf( (isoprenoid metabolic process) AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways involving isoprenoid compounds, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "GO:0016096") AnnotationAssertion( "isoprenoid metabolism") AnnotationAssertion( "polyisoprenoid metabolic process") @@ -13674,7 +13775,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006720") AnnotationAssertion(rdfs:label "isoprenoid metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (terpenoid metabolic process) @@ -13755,7 +13856,7 @@ AnnotationAssertion( "GO:0006793") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "phosphorus metabolic process") -SubClassOf( ) +SubClassOf( ) # Class: (phosphate-containing compound metabolic process) @@ -13782,7 +13883,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "xenobiotic metabolic process") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (transport) @@ -14094,7 +14195,6 @@ SubClassOf( ObjectSomeValuesFrom( "ISBN:0198506732") "A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24907"^^xsd:anyURI) -AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Phagocytosis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006909") @@ -14129,14 +14229,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "autophagy") -SubClassOf( ) +SubClassOf( ) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (apoptotic process) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dhl") Annotation( "GOC:ecd") Annotation( "GOC:go_curators") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:tb") Annotation( "ISBN:0198506732") Annotation( "PMID:18846107") Annotation( "PMID:21494263") "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "GO:0006917") AnnotationAssertion( "GO:0008632") AnnotationAssertion( "cell suicide") @@ -14160,6 +14259,21 @@ AnnotationAssertion( "GO:0006915") AnnotationAssertion(rdfs:label "apoptotic process") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular component disassembly involved in execution phase of apoptosis) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:tb") "The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.") +AnnotationAssertion( "cellular component disassembly involved in apoptotic process") +AnnotationAssertion( "disassembly of cell structures") +AnnotationAssertion( "cellular component disassembly involved in apoptosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006921") +AnnotationAssertion(rdfs:label "cellular component disassembly involved in execution phase of apoptosis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (activation-induced cell death of T cells) @@ -14756,7 +14870,6 @@ SubClassOf( ObjectSomeValuesFrom( (male meiotic nuclear division) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:vw") "A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline.") -AnnotationAssertion( ) AnnotationAssertion( "male nuclear division") AnnotationAssertion( "biological_process") AnnotationAssertion( "male meiosis") @@ -14769,7 +14882,6 @@ SubClassOf( ObjectSomeValuesFrom( (female meiotic nuclear division) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:ems") Annotation( "GOC:mah") Annotation( "GOC:vw") "A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline.") -AnnotationAssertion( ) AnnotationAssertion( "female meiosis") AnnotationAssertion( "female meiotic division") AnnotationAssertion( "biological_process") @@ -14966,9 +15078,6 @@ SubClassOf( (gamete generation) AnnotationAssertion(Annotation( "GOC:ems") Annotation( "GOC:mtg_sensu") "The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "GO:0009552") AnnotationAssertion( "biological_process") AnnotationAssertion( "gametogenesis") @@ -15047,7 +15156,6 @@ SubClassOf( ObjectSomeValuesFrom( (single fertilization) AnnotationAssertion(Annotation( "GOC:ems") Annotation( "GOC:mtg_sensu") "The union of male and female gametes to form a zygote.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "zygote biosynthesis") AnnotationAssertion( "zygote formation") @@ -15074,6 +15182,8 @@ AnnotationAssertion(rdfs:comment "If AnnotationAssertion(rdfs:label "acrosome reaction") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (penetration of zona pellucida) @@ -15867,19 +15977,16 @@ AnnotationAssertion(rdfs:label "biol # Class: (metabolic process) -AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198547684") "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.") +AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28932"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-17T15:46:40Z") AnnotationAssertion( "GO:0044236") AnnotationAssertion( "GO:0044710") AnnotationAssertion( "Wikipedia:Metabolism") AnnotationAssertion( "metabolism") -AnnotationAssertion( "metabolic process resulting in cell growth") -AnnotationAssertion( "metabolism resulting in cell growth") -AnnotationAssertion( "multicellular organism metabolic process") AnnotationAssertion( "biological_process") -AnnotationAssertion( "single-organism metabolic process") AnnotationAssertion( "GO:0008152") AnnotationAssertion( ) AnnotationAssertion( ) @@ -15890,7 +15997,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.") AnnotationAssertion(rdfs:label "metabolic process") -SubClassOf( ) +SubClassOf( ) DisjointClasses( ) DisjointClasses( ) @@ -15976,8 +16083,6 @@ SubClassOf( (cholesterol metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "cholesterol metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0008203") @@ -16014,7 +16119,6 @@ SubClassOf( (cell population proliferation) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:mb") "The multiplication or reproduction of cells, resulting in the expansion of a cell population.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "cell proliferation") AnnotationAssertion( "GO:0008283") @@ -16031,7 +16135,6 @@ SubClassOf( (positive regulation of cell population proliferation) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the rate or extent of cell proliferation.") -AnnotationAssertion( ) AnnotationAssertion( "up regulation of cell proliferation") AnnotationAssertion( "up-regulation of cell proliferation") AnnotationAssertion( "upregulation of cell proliferation") @@ -16049,7 +16152,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of cell population proliferation) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents or reduces the rate or extent of cell proliferation.") -AnnotationAssertion( ) AnnotationAssertion( "down regulation of cell proliferation") AnnotationAssertion( "down-regulation of cell proliferation") AnnotationAssertion( "downregulation of cell proliferation") @@ -16157,7 +16259,7 @@ AnnotationAssertion(Annotation( "EC:3.1.2.22") AnnotationAssertion( "MetaCyc:3.1.2.22-RXN") AnnotationAssertion( "RHEA:19233") -AnnotationAssertion(Annotation(rdfs:label "depalmitoylation of eNOS") "Reactome:R-HSA-203613") +AnnotationAssertion(Annotation(rdfs:label "Depalmitoylation of eNOS") "Reactome:R-HSA-203613") AnnotationAssertion(Annotation(rdfs:label "PPT1 hydrolyses palmitoylated proteins") "Reactome:R-HSA-5690517") AnnotationAssertion(Annotation(rdfs:label "LYPLA2 hydrolyses PALM-C3,4-GAP43") "Reactome:R-HSA-8933328") AnnotationAssertion(Annotation(rdfs:label "RAS proteins are depalmitoylated") "Reactome:R-HSA-9647994") @@ -16188,7 +16290,6 @@ SubClassOf( ObjectSomeValuesFrom( (epidermis development) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "UBERON:0001003") "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "GOC:rk") "hypodermis development") AnnotationAssertion( "GO:0008544") @@ -16207,8 +16308,6 @@ AnnotationAssertion(Annotation( "EC:7.2.2.3") "sodium transport ATPase activity") AnnotationAssertion(Annotation( "EC:7.2.2.3") "sodium-exporting ATPase activity") AnnotationAssertion( "EC:7.2.2.3") -AnnotationAssertion( "MetaCyc:RXN-17739") -AnnotationAssertion( "RHEA:14633") AnnotationAssertion( "sodium exporting ATPase activity, phosphorylative mechanism") AnnotationAssertion( "sodium transmembrane transporter activity, phosphorylative mechanism") AnnotationAssertion( "sodium-exporting ATPase activity, phosphorylative mechanism") @@ -16264,7 +16363,6 @@ SubClassOf( ObjectSomeValuesFrom( (female gonad development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") Annotation( "GOC:tb") "The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.") -AnnotationAssertion( ) AnnotationAssertion( "GO:0061039") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:sl") "ovarian development") @@ -16347,7 +16445,6 @@ SubClassOf( "GOC:jl") Annotation( "GOC:mr") Annotation( "GOC:pr") Annotation( "PMID:11498577") Annotation( "PMID:20622855") Annotation( "Wikipedia:XY_sex-determination_system") "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by heterochromatin formation leading to a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25955"^^xsd:anyURI) -AnnotationAssertion( ) AnnotationAssertion( "chromosome inactivation") AnnotationAssertion( "Wikipedia:X-inactivation") AnnotationAssertion( "X chromosome inactivation") @@ -16360,18 +16457,20 @@ SubClassOf( (catabolic process) -AnnotationAssertion(Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.") +AnnotationAssertion(Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism breaks down substances. This includes the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28921"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28932"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-17T15:52:35Z") AnnotationAssertion( "GO:0044243") AnnotationAssertion( "GO:0044712") AnnotationAssertion( "Wikipedia:Catabolism") -AnnotationAssertion( "breakdown") +AnnotationAssertion( "breakdown of chemical") +AnnotationAssertion( "breakdown of molecule") +AnnotationAssertion( "breakdown of substance") AnnotationAssertion( "catabolism") AnnotationAssertion( "degradation") -AnnotationAssertion( "multicellular organismal catabolic process") AnnotationAssertion( "biological_process") -AnnotationAssertion( "single-organism catabolic process") AnnotationAssertion( "GO:0009056") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16402,7 +16501,8 @@ SubClassOf( (biosynthetic process) -AnnotationAssertion(Annotation( "GOC:curators") Annotation( "ISBN:0198547684") "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.") +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28932"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-17T15:52:18Z") AnnotationAssertion( "GO:0044274") @@ -16441,8 +16541,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") AnnotationAssertion(rdfs:label "macromolecule biosynthetic process") +SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (aerobic respiration) @@ -16457,6 +16557,7 @@ SubClassOf( (fatty acid catabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways resulting in the breakdown of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Fatty_acid_degradation") AnnotationAssertion( "fatty acid breakdown") AnnotationAssertion( "fatty acid catabolism") @@ -16465,7 +16566,7 @@ AnnotationAssertion( "GO:0009062") AnnotationAssertion(rdfs:label "fatty acid catabolic process") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (nucleoside metabolic process) @@ -16813,21 +16914,6 @@ SubClassOf( ) SubClassOf( ) -# Class: (amine metabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2009-07-15T11:55:44Z") -AnnotationAssertion( "GO:0044106") -AnnotationAssertion( "amine metabolism") -AnnotationAssertion( "cellular amine metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0009308") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "amine metabolic process") -SubClassOf( ) - # Class: (response to radiation) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "Wikipedia:Electromagnetic_radiation") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.") @@ -16842,6 +16928,7 @@ SubClassOf( (phospholipid catabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "phospholipid breakdown") AnnotationAssertion( "phospholipid catabolism") AnnotationAssertion( "phospholipid degradation") @@ -16849,7 +16936,7 @@ AnnotationAssertion( "GO:0009395") AnnotationAssertion(rdfs:label "phospholipid catabolic process") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (response to xenobiotic stimulus) @@ -17043,8 +17130,6 @@ SubClassOf( (response to hormone) AnnotationAssertion(Annotation( "GOC:jl") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(Annotation( "GOC:dos") "response to hormone stimulus") AnnotationAssertion( "biological_process") AnnotationAssertion( "growth regulator") @@ -17128,11 +17213,6 @@ SubClassOf( ObjectSomeValuesFrom( (tissue development) AnnotationAssertion(Annotation( "ISBN:0471245208") "The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "histogenesis and organogenesis") AnnotationAssertion( "Wikipedia:Histogenesis") AnnotationAssertion( "histogenesis") @@ -17211,7 +17291,7 @@ AnnotationAssertion( "negative regulation of metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of metabolic process) @@ -17233,7 +17313,7 @@ AnnotationAssertion( "positive regulation of metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of catabolic process) @@ -17659,7 +17739,7 @@ AnnotationAssertion( "GO:0010506") AnnotationAssertion(rdfs:label "regulation of autophagy") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of autophagy) @@ -17669,8 +17749,8 @@ AnnotationAssertion( "GO:0010507") AnnotationAssertion(rdfs:label "negative regulation of autophagy") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of autophagy) @@ -17680,8 +17760,8 @@ AnnotationAssertion( "GO:0010508") AnnotationAssertion(rdfs:label "positive regulation of autophagy") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of platelet activation) @@ -17713,7 +17793,7 @@ AnnotationAssertion( "GO:0010556") AnnotationAssertion(rdfs:label "regulation of macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -17724,9 +17804,9 @@ AnnotationAssertion( "GO:0010557") AnnotationAssertion(rdfs:label "positive regulation of macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of macromolecule biosynthetic process) @@ -17736,9 +17816,9 @@ AnnotationAssertion( "GO:0010558") AnnotationAssertion(rdfs:label "negative regulation of macromolecule biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of phosphorus metabolic process) @@ -17748,7 +17828,7 @@ AnnotationAssertion( "GO:0010562") AnnotationAssertion(rdfs:label "positive regulation of phosphorus metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -17759,7 +17839,7 @@ AnnotationAssertion( "GO:0010563") AnnotationAssertion(rdfs:label "negative regulation of phosphorus metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -17773,15 +17853,15 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of cellular ketone metabolic process) +# Class: (regulation of ketone metabolic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010565") -AnnotationAssertion(rdfs:label "regulation of cellular ketone metabolic process") +AnnotationAssertion(rdfs:label "regulation of ketone metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of nuclear cell cycle DNA replication) @@ -18959,6 +19039,7 @@ AnnotationAssertion( "Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.") AnnotationAssertion(rdfs:label "programmed cell death") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (endomembrane system) @@ -19360,7 +19441,6 @@ SubClassOf( (urinary bladder smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:mr") Annotation( "GOC:mtg_muscle") Annotation( "PMID:11768524") Annotation( "PMID:18276178") Annotation( "PMID:538956") "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the urinary bladder. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The urinary bladder is a musculomembranous sac along the urinary tract.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0014832") AnnotationAssertion(rdfs:label "urinary bladder smooth muscle contraction") @@ -19574,9 +19654,10 @@ AnnotationAssertion(Annotation( "Reactome:R-HSA-1222516") AnnotationAssertion(Annotation(rdfs:label "Enzyme-bound ATP is released") "Reactome:R-HSA-164834") AnnotationAssertion(Annotation(rdfs:label "Virion-associated M2 protein mediated ion infusion") "Reactome:R-HSA-168313") -AnnotationAssertion(Annotation(rdfs:label "Protons are translocated from the intermembrane space to the matrix") "Reactome:R-HSA-170026") +AnnotationAssertion(Annotation(rdfs:label "UCP1 imports a proton") "Reactome:R-HSA-170026") AnnotationAssertion(Annotation(rdfs:label "Endosome acidification") "Reactome:R-HSA-74723") AnnotationAssertion(Annotation(rdfs:label "Acidification of Tf:TfR1 containing endosome") "Reactome:R-HSA-917841") +AnnotationAssertion(Annotation(rdfs:label "AAC1 imports a proton") "Reactome:R-HSA-9864415") AnnotationAssertion( "hydrogen ion transmembrane transporter activity") AnnotationAssertion( "proton transporter activity") AnnotationAssertion( "molecular_function") @@ -19589,9 +19670,9 @@ SubClassOf( ObjectSomeValuesFrom( (potassium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:ai") "Enables the transfer of potassium ions (K+) from one side of a membrane to the other.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27521"^^xsd:anyURI) AnnotationAssertion( "GO:0015388") AnnotationAssertion( "GO:0022817") -AnnotationAssertion( "RHEA:29463") AnnotationAssertion( "potassium transporter activity") AnnotationAssertion( "molecular_function") AnnotationAssertion( "potassium uptake permease activity") @@ -19603,10 +19684,10 @@ SubClassOf( ObjectSomeValuesFrom( (sodium ion transmembrane transporter activity) -AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:ai") Annotation( "RHEA:34963") "Enables the transfer of sodium ions (Na+) from one side of a membrane to the other.") +AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:ai") "Enables the transfer of sodium ions (Na+) from one side of a membrane to the other.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24076"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27521"^^xsd:anyURI) AnnotationAssertion( "GO:0022816") -AnnotationAssertion( "RHEA:34963") AnnotationAssertion( "sodium transporter activity") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0015081") @@ -19627,8 +19708,8 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:ai") "Enables the transfer of chloride ions from one side of a membrane to the other.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20821"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27521"^^xsd:anyURI) AnnotationAssertion( "GO:0008555") -AnnotationAssertion( "RHEA:29823") AnnotationAssertion(Annotation(rdfs:label "Defective CFTR does not transport Cl- from cytosol to extracellular region") "Reactome:R-HSA-5678822") AnnotationAssertion(Annotation(rdfs:label "CFTR transports Cl- from cytosol to extracellular region") "Reactome:R-HSA-5678863") AnnotationAssertion(Annotation(rdfs:label "Ivacaftor:CFTR G551D transports Cl- from cytosol to extracellular region") "Reactome:R-HSA-5678992") @@ -19668,7 +19749,7 @@ SubClassOf( (calcium-activated potassium channel activity) -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_transport") "Enables the calcium concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_transport") "Enables the transmembrane transfer of a potassium cation by a channel that opens when a calcium cation has been bound by the channel complex or one of its constituent parts.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24605"^^xsd:anyURI) AnnotationAssertion(Annotation(rdfs:label "KCNN2 transports K+ from the cytosol to the extracellular region") "Reactome:R-HSA-9663752") AnnotationAssertion(Annotation(rdfs:label "KCNMA1:KCNMB1 transports potassium ions from the cytosol to the extracellular region") "Reactome:R-HSA-9667809") @@ -19909,6 +19990,18 @@ AnnotationAssertion( "microtubule cytoskeleton") SubClassOf( ) +# Class: (fatty acid ligase activity) + +AnnotationAssertion(Annotation( "GOC:cjk") Annotation( "GOC:mah") "Catalysis of the ligation of a fatty acid to an acceptor, coupled to the hydrolysis of ATP.") +AnnotationAssertion( "fatty-acid ligase activity") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "fatty acid CoA ligase activity") +AnnotationAssertion( "fatty acyl-coenzyme A synthetase activity") +AnnotationAssertion( "GO:0015645") +AnnotationAssertion(rdfs:label "fatty acid ligase activity") +SubClassOf( ) +SubClassOf( ) + # Class: (P-type ion transporter activity) AnnotationAssertion(Annotation( "PMID:10322420") Annotation( "PMID:10600683") "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O = ADP + phosphate, to directly drive the transport of ions across a membrane. The reaction is characterized by the transient formation of a high-energy aspartyl-phosphoryl-enzyme intermediate.") @@ -20340,7 +20433,6 @@ SubClassOf( (catechol O-methyltransferase activity) AnnotationAssertion(Annotation( "EC:2.1.1.6") Annotation( "RHEA:17877") "Catalysis of the reaction: a catechol + S-adenosyl-L-methionine = a guaiacol + H+ + S-adenosyl-L-homocysteine. Acts on catechols and on catecholamines such as adrenaline or noradrenaline.") -AnnotationAssertion( ) AnnotationAssertion( "EC:2.1.1.6") AnnotationAssertion( "MetaCyc:CATECHOL-O-METHYLTRANSFERASE-RXN") AnnotationAssertion( "RHEA:17877") @@ -20387,6 +20479,7 @@ AnnotationAssertion( "GO:0016236") AnnotationAssertion(rdfs:label "macroautophagy") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of macroautophagy) @@ -20444,7 +20537,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lipase activity") -SubClassOf( ) +SubClassOf( ) # Class: (kinase activity) @@ -20527,6 +20620,7 @@ AnnotationAssertion(Annotation(rdfs:label "KAT5 acetylates ATM at DNA DSBs") "Reactome:R-HSA-6792712") AnnotationAssertion(Annotation(rdfs:label "KAT6A acetylates TP53") "Reactome:R-HSA-6805638") AnnotationAssertion(Annotation(rdfs:label "Acetylation of SL1") "Reactome:R-HSA-73736") +AnnotationAssertion(Annotation(rdfs:label "ACAT1 tetramer acetylates IDH2 dimer") "Reactome:R-HSA-9854415") AnnotationAssertion( "acetylase activity") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0016407") @@ -20537,6 +20631,8 @@ SubClassOf( "GOC:ai") "Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule.") AnnotationAssertion(Annotation(rdfs:label "phenylacetyl-CoA + glutamine => phenylacetyl glutamine + Coenzyme A") "Reactome:R-HSA-177160") +AnnotationAssertion(Annotation(rdfs:label "LIPT1 transfers lipoyl group from lipoyl-GCSH to DBT/DLST") "Reactome:R-HSA-6792572") +AnnotationAssertion(Annotation(rdfs:label "LIPT1 transfers lipoyl group from lipoyl-GCSH to DLAT") "Reactome:R-HSA-9858752") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0016410") AnnotationAssertion(rdfs:label "N-acyltransferase activity") @@ -20554,7 +20650,6 @@ SubClassOf( (somatic cell DNA recombination) AnnotationAssertion(Annotation( "GOC:ma") "Recombination occurring within or between DNA molecules in somatic cells.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0016444") AnnotationAssertion(rdfs:label "somatic cell DNA recombination") @@ -20603,7 +20698,6 @@ SubClassOf( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:ems") Annotation( "GOC:pf") Annotation( "Wikipedia:Cell_migration") "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24787"^^xsd:anyURI) -AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Cell_migration") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0016477") @@ -20617,14 +20711,16 @@ AnnotationAssertion( "Reactome:R-HSA-1614362") AnnotationAssertion(Annotation(rdfs:label "Monoiodinated tyrosine can be deiodinated") "Reactome:R-HSA-209921") AnnotationAssertion(Annotation(rdfs:label "Diiodinated tyrosine can be deiodinated") "Reactome:R-HSA-209960") -AnnotationAssertion(Annotation(rdfs:label "MMACHC dealkylates RCbl") "Reactome:R-HSA-3095889") +AnnotationAssertion(Annotation(rdfs:label "PGH2 is reduced to PGF2a by FAM213B") "Reactome:R-HSA-2161612") +AnnotationAssertion(Annotation(rdfs:label "Arachidonate is oxidised to 5S-HpETE by ALOX5") "Reactome:R-HSA-265296") +AnnotationAssertion(Annotation(rdfs:label "5S-HpETE is dehydrated to LTA4 by ALOX5") "Reactome:R-HSA-266051") AnnotationAssertion(Annotation(rdfs:label "FAR1 reduces PalmCoA to HXOL") "Reactome:R-HSA-390425") AnnotationAssertion(Annotation(rdfs:label "FAR2 reduces PalmCoA to HXOL") "Reactome:R-HSA-390438") AnnotationAssertion(Annotation(rdfs:label "Dopachrome is transformed to DHICA by DCT") "Reactome:R-HSA-5662660") AnnotationAssertion(Annotation(rdfs:label "TYRP1 oxidises DHICA to IQCA") "Reactome:R-HSA-8878581") AnnotationAssertion(Annotation(rdfs:label "MARC1,MARC2 reduce N-hydroxylated compounds") "Reactome:R-HSA-8936442") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6") "Reactome:R-HSA-9020249") -AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reducatse reduces 7(S)-Hp-17(S)-HDHA to RvD5") "Reactome:R-HSA-9020260") +AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 7(S)-Hp-17(S)-HDHA to RvD5") "Reactome:R-HSA-9020260") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6") "Reactome:R-HSA-9024624") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5") "Reactome:R-HSA-9024630") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1") "Reactome:R-HSA-9025007") @@ -20632,6 +20728,7 @@ AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reductase reduces 7,17-di AnnotationAssertion(Annotation(rdfs:label "Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA") "Reactome:R-HSA-9026917") AnnotationAssertion(Annotation(rdfs:label "Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA") "Reactome:R-HSA-9027033") AnnotationAssertion(Annotation(rdfs:label "Unknown sepiapterin synthase transforms PTHP to sepiapterin") "Reactome:R-HSA-9693722") +AnnotationAssertion(Annotation(rdfs:label "Cob(I)alamin bound to MMACHC is oxidized to cob(II)alamin") "Reactome:R-HSA-9759549") AnnotationAssertion( "redox activity") AnnotationAssertion( "oxidoreductase activity, acting on other substrates") AnnotationAssertion( "molecular_function") @@ -20666,7 +20763,6 @@ SubClassOf( ObjectSomeValuesFrom( (sarcoplasm) AnnotationAssertion(Annotation( "ISBN:0198547684") "The cytoplasm of a muscle cell; includes the sarcoplasmic reticulum.") -AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Sarcoplasm") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0016528") @@ -20741,7 +20837,7 @@ SubClassOf( (oxidoreductase activity, acting on the CH-NH2 group of donors) -AnnotationAssertion(Annotation( "GOC:ai") "Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.") +AnnotationAssertion(Annotation( "EC:1.4.-.-") Annotation( "GOC:ai") "Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.") AnnotationAssertion( "EC:1.4.-.-") AnnotationAssertion( "oxidoreductase activity, acting on the CH-NH2 group of donors, other acceptors") AnnotationAssertion( "molecular_function") @@ -20871,7 +20967,6 @@ AnnotationAssertion( "Reactome:R-HSA-159431") AnnotationAssertion(Annotation(rdfs:label "Choloyl CoA reacts with glycine or taurine to form glycocholate or taurocholate") "Reactome:R-HSA-192312") AnnotationAssertion(Annotation(rdfs:label "Chenodeoxycholoyl CoA reacts with glycine or taurine to form glycochenodeoxycholate or taurochenodeoxycholate") "Reactome:R-HSA-193491") -AnnotationAssertion(Annotation(rdfs:label "LIPT1 transfers lipoyl group from lipoyl-GCSH to DHs") "Reactome:R-HSA-6792572") AnnotationAssertion(Annotation(rdfs:label "HRASLS transfer acyl group from PC to PE to form NAPE") "Reactome:R-HSA-8858298") AnnotationAssertion( "transferase activity, transferring acyl groups") AnnotationAssertion( "molecular_function") @@ -20886,6 +20981,8 @@ SubClassOf( "EC:2.3.1.-") "Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20486"^^xsd:anyURI) AnnotationAssertion( "EC:2.3.1.-") +AnnotationAssertion(Annotation(rdfs:label "DBT transfers BCAA to CoA") "Reactome:R-HSA-9859163") +AnnotationAssertion(Annotation(rdfs:label "DBT loss-of-function mutants don't synthesize BCAA-CoA") "Reactome:R-HSA-9865115") AnnotationAssertion( "transferase activity, transferring acyl groups other than amino-acyl groups") AnnotationAssertion( "molecular_function") AnnotationAssertion(Annotation( "EC:2.3.1.-") "transferase activity, transferring groups other than amino-acyl groups") @@ -20957,7 +21054,7 @@ SubClassOf( "EC:2.5.1.-") "Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).") AnnotationAssertion( "GO:0016766") AnnotationAssertion( "EC:2.5.1.-") -AnnotationAssertion(Annotation(rdfs:label "MMAB adenosylates cob(I)alamin") "Reactome:R-HSA-3159253") +AnnotationAssertion(Annotation(rdfs:label "MMACHC dealkylates RCbl") "Reactome:R-HSA-3095889") AnnotationAssertion(Annotation(rdfs:label "DHDDS:NUS1 elongates E,E-FPP with (n)IPPP to form pPPP") "Reactome:R-HSA-4419978") AnnotationAssertion(Annotation(rdfs:label "Defective DHDDS does not elongate E,E-FPP") "Reactome:R-HSA-4755545") AnnotationAssertion(Annotation(rdfs:label "TRMT12 transforms yW-187 yielding yW-86 at nucleotide 37 of tRNA(Phe)") "Reactome:R-HSA-6782893") @@ -21128,6 +21225,8 @@ SubClassOf( "GOC:jl") "Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.") AnnotationAssertion( "EC:4.1.-.-") +AnnotationAssertion(Annotation(rdfs:label "UROD decarboxylates URO3 to COPRO3") "Reactome:R-HSA-189425") +AnnotationAssertion(Annotation(rdfs:label "UROD decarboxylates URO1 to COPRO1") "Reactome:R-HSA-190182") AnnotationAssertion(Annotation(rdfs:label "2-hydroxyphytanoyl-CoA => pristanal + formyl-CoA") "Reactome:R-HSA-389611") AnnotationAssertion( "other carbon-carbon lyase activity") AnnotationAssertion( "molecular_function") @@ -21162,6 +21261,7 @@ SubClassOf( "EC:4.2.1.-") "Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.") AnnotationAssertion( "EC:4.2.1.-") +AnnotationAssertion(Annotation(rdfs:label "PGE2 is dehydrated to PGA2") "Reactome:R-HSA-2161659") AnnotationAssertion(Annotation(rdfs:label "SDS dimers:PXLP dehydrate L-Thr to 2AA") "Reactome:R-HSA-9014627") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0016836") @@ -21172,6 +21272,8 @@ SubClassOf( "ISBN:0198506732") "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.") AnnotationAssertion( "EC:5.-.-.-") +AnnotationAssertion(Annotation(rdfs:label "PGA2 is isomerised to PGC2") "Reactome:R-HSA-2161666") +AnnotationAssertion(Annotation(rdfs:label "PGC2 is isomerised to PGB2") "Reactome:R-HSA-2161735") AnnotationAssertion(Annotation(rdfs:label "TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal") "Reactome:R-HSA-6787623") AnnotationAssertion( "other isomerase activity") AnnotationAssertion( "molecular_function") @@ -21242,6 +21344,15 @@ AnnotationAssertion( "ligase activity, forming carbon-sulfur bonds") SubClassOf( ) +# Class: (acid-thiol ligase activity) + +AnnotationAssertion(Annotation( "EC:6.2.1.-") Annotation( "GOC:mah") "Catalysis of the joining of an acid and a thiol via a carbon-sulfur bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.") +AnnotationAssertion( "EC:6.2.1.-") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0016878") +AnnotationAssertion(rdfs:label "acid-thiol ligase activity") +SubClassOf( ) + # Class: (ATP hydrolysis activity) AnnotationAssertion(Annotation( "RHEA:13065") "Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.") @@ -21328,9 +21439,6 @@ SubClassOf( (stem cell division) AnnotationAssertion(Annotation( "GOC:jid") Annotation( "ISBN:0582227089") "The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "stem cell renewal") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0017145") @@ -21361,6 +21469,16 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (calcium-ion regulated exocytosis) + +AnnotationAssertion(Annotation( "GOC:go_curators") "The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels.") +AnnotationAssertion( "calcium ion-dependent exocytosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0017156") +AnnotationAssertion(rdfs:comment "Note that the calcium regulated exocytosis pathway can be leaky: some level of exocytosis via this pathway occurs spontaneously. This phenomenon underlies spontaneous neurotransmitter release from presynapses. This phenomenon is distinct from the unregulated, calcium independent exocytosis pathway.") +AnnotationAssertion(rdfs:label "calcium-ion regulated exocytosis") +SubClassOf( ) + # Class: (regulation of exocytosis) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of exocytosis.") @@ -21372,6 +21490,16 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of calcium ion-dependent exocytosis) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of calcium ion-dependent exocytosis.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0017158") +AnnotationAssertion(rdfs:label "regulation of calcium ion-dependent exocytosis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (nicotine metabolic process) AnnotationAssertion(Annotation( "GOC:sm") Annotation( "ISBN:0198547684") "The chemical reactions and pathways involving nicotine, (S)(-)-3-(1-methyl-2-pyrrolidinyl)pyridine.") @@ -21477,6 +21605,7 @@ AnnotationAssertion(rdfs:label "regu EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of steroid metabolic process) @@ -21525,7 +21654,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "regulation of metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (transmission of nerve impulse) @@ -21702,7 +21831,6 @@ AnnotationAssertion( "regulation of isoprenoid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (secondary metabolic process) @@ -22557,12 +22685,25 @@ AnnotationAssertion( "ribonucleoprotein complex biogenesis") SubClassOf( ) +# Class: (protein-RNA complex assembly) + +AnnotationAssertion(Annotation( "GOC:jl") "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.") +AnnotationAssertion( "RNA-protein complex assembly") +AnnotationAssertion( "RNP complex assembly") +AnnotationAssertion( "ribonucleoprotein complex assembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0022618") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "protein-RNA complex assembly") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (passive transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:mtg_transport") Annotation( "ISBN:0815340729") "Enables the transfer of a single solute from one side of a membrane to the other by a mechanism involving conformational change, either by facilitated diffusion or in a membrane potential dependent process if the solute is charged.") AnnotationAssertion( "GO:0022814") AnnotationAssertion( "porters") -AnnotationAssertion(Annotation(rdfs:label "Passive I- efflux mediated by SMCT1") "Reactome:R-HSA-429767") AnnotationAssertion( "Wikipedia:Facilitated_diffusion") AnnotationAssertion( "uniporter activity z") AnnotationAssertion( "molecular_function") @@ -22881,6 +23022,17 @@ AnnotationAssertion( "cell projection organization") SubClassOf( ) +# Class: (cell projection assembly) + +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") +AnnotationAssertion( "GO:0030031") +AnnotationAssertion(rdfs:label "cell projection assembly") +SubClassOf( ) +SubClassOf( ) + # Class: (actin filament-based movement) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins.") @@ -22893,7 +23045,6 @@ SubClassOf( (cell junction) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "GOC:mah") Annotation( "ISBN:0198506732") Annotation( "PMID:26820516") Annotation( "PMID:28096264") "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.") -AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Cell_junction") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0030054") @@ -23032,7 +23183,6 @@ SubClassOf( ObjectSomeValuesFrom( (secretory granule) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0198506732") "A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.") -AnnotationAssertion( ) AnnotationAssertion( "secretory vesicle") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0030141") @@ -23268,10 +23418,11 @@ SubClassOf( (lipid modification) AnnotationAssertion(Annotation( "GOC:mah") "The covalent alteration of one or more fatty acids in a lipid, resulting in a change in the properties of the lipid.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0030258") AnnotationAssertion(rdfs:label "lipid modification") -SubClassOf( ) +SubClassOf( ) # Class: (regulation of ossification) @@ -23475,7 +23626,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cell migration) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of cell migration.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0030334") AnnotationAssertion(rdfs:label "regulation of cell migration") @@ -24292,7 +24442,6 @@ SubClassOf( (developmental induction) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "PMID:24503535") "A developmental process involving two tissues in which one tissue (the inducer) produces a signal that directs cell fate commitment of cells in the second tissue (the responder).") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0031128") AnnotationAssertion(rdfs:label "developmental induction") @@ -24369,189 +24518,6 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (regulation of cellular metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "regulation of cellular metabolism") -AnnotationAssertion( "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( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of cellular metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "down regulation of cellular metabolic process") -AnnotationAssertion( "down-regulation of cellular metabolic process") -AnnotationAssertion( "downregulation of cellular metabolic process") -AnnotationAssertion( "negative regulation of cellular metabolism") -AnnotationAssertion( "inhibition of cellular metabolic process") -AnnotationAssertion( "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( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of cellular metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "positive regulation of cellular metabolism") -AnnotationAssertion( "up regulation of cellular metabolic process") -AnnotationAssertion( "up-regulation of cellular metabolic process") -AnnotationAssertion( "upregulation of cellular metabolic process") -AnnotationAssertion( "activation of cellular metabolic process") -AnnotationAssertion( "stimulation of cellular metabolic process") -AnnotationAssertion( "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( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (regulation of cellular biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "regulation of cellular anabolism") -AnnotationAssertion( "regulation of cellular biosynthesis") -AnnotationAssertion( "regulation of cellular formation") -AnnotationAssertion( "regulation of cellular synthesis") -AnnotationAssertion( "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( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of cellular biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "down regulation of cellular biosynthetic process") -AnnotationAssertion( "down-regulation of cellular biosynthetic process") -AnnotationAssertion( "downregulation of cellular biosynthetic process") -AnnotationAssertion( "negative regulation of cellular anabolism") -AnnotationAssertion( "negative regulation of cellular biosynthesis") -AnnotationAssertion( "negative regulation of cellular formation") -AnnotationAssertion( "negative regulation of cellular synthesis") -AnnotationAssertion( "inhibition of cellular biosynthetic process") -AnnotationAssertion( "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( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of cellular biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "positive regulation of cellular anabolism") -AnnotationAssertion( "positive regulation of cellular biosynthesis") -AnnotationAssertion( "positive regulation of cellular formation") -AnnotationAssertion( "positive regulation of cellular synthesis") -AnnotationAssertion( "up regulation of cellular biosynthetic process") -AnnotationAssertion( "up-regulation of cellular biosynthetic process") -AnnotationAssertion( "upregulation of cellular biosynthetic process") -AnnotationAssertion( "activation of cellular biosynthetic process") -AnnotationAssertion( "stimulation of cellular biosynthetic process") -AnnotationAssertion( "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( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (regulation of cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "regulation of cellular breakdown") -AnnotationAssertion( "regulation of cellular catabolism") -AnnotationAssertion( "regulation of cellular degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031329") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "regulation of cellular catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "down regulation of cellular catabolic process") -AnnotationAssertion( "down-regulation of cellular catabolic process") -AnnotationAssertion( "downregulation of cellular catabolic process") -AnnotationAssertion( "negative regulation of cellular breakdown") -AnnotationAssertion( "negative regulation of cellular catabolism") -AnnotationAssertion( "negative regulation of cellular degradation") -AnnotationAssertion( "inhibition of cellular catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031330") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "negative regulation of cellular catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of cellular catabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "positive regulation of cellular breakdown") -AnnotationAssertion( "positive regulation of cellular catabolism") -AnnotationAssertion( "positive regulation of cellular degradation") -AnnotationAssertion( "up regulation of cellular catabolic process") -AnnotationAssertion( "up-regulation of cellular catabolic process") -AnnotationAssertion( "upregulation of cellular catabolic process") -AnnotationAssertion( "activation of cellular catabolic process") -AnnotationAssertion( "stimulation of cellular catabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0031331") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") -AnnotationAssertion(rdfs:label "positive regulation of cellular catabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (negative regulation of protein-containing complex assembly) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.") @@ -24890,6 +24856,7 @@ AnnotationAssertion( "GO:0031507") AnnotationAssertion(rdfs:label "heterochromatin formation") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (motile cilium) @@ -25212,7 +25179,6 @@ AnnotationAssertion( "GO:0031998") AnnotationAssertion(rdfs:label "regulation of fatty acid beta-oxidation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -25228,7 +25194,6 @@ AnnotationAssertion( "GO:0031999") AnnotationAssertion(rdfs:label "negative regulation of fatty acid beta-oxidation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -25246,7 +25211,6 @@ AnnotationAssertion( "GO:0032000") AnnotationAssertion(rdfs:label "positive regulation of fatty acid beta-oxidation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -25312,6 +25276,48 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (negative regulation of translational initiation in response to stress) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents or reduces the rate of translation initiation as a result of a stimulus indicating the organism is under stress.") +AnnotationAssertion( "down regulation of translation initiation in response to stress") +AnnotationAssertion( "down-regulation of translation initiation in response to stress") +AnnotationAssertion( "downregulation of translation initiation in response to stress") +AnnotationAssertion( "inhibition of translation initiation in response to stress") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032057") +AnnotationAssertion(rdfs:label "negative regulation of translational initiation in response to stress") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translational initiation in response to stress) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of translation initiation as a result of a stimulus indicating the organism is under stress.") +AnnotationAssertion( "up regulation of translation initiation in response to stress") +AnnotationAssertion( "up-regulation of translation initiation in response to stress") +AnnotationAssertion( "upregulation of translation initiation in response to stress") +AnnotationAssertion( "activation of translation initiation in response to stress") +AnnotationAssertion( "stimulation of translation initiation in response to stress") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032058") +AnnotationAssertion(rdfs:label "positive regulation of translational initiation in response to stress") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (bleb assembly) + +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:12083798") Annotation( "PMID:16624291") Annotation( "Wikipedia:Bleb_(cell_biology)") "The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.") +AnnotationAssertion(Annotation( "GOC:pr") "blebbing") +AnnotationAssertion(Annotation( "GOC:pr") "membrane blebbing") +AnnotationAssertion( "cell blebbing") +AnnotationAssertion(Annotation( "GOC:pr") "plasma membrane bleb assembly") +AnnotationAssertion(Annotation( "GOC:pr") "plasma membrane blebbing") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032060") +AnnotationAssertion(rdfs:label "bleb assembly") +SubClassOf( ) + # Class: (negative regulation of translation in response to osmotic stress) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents or reduces the rate of translation as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.") @@ -25341,6 +25347,37 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (negative regulation of translational initiation in response to osmotic stress) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents or reduces the rate of translation initiation, as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.") +AnnotationAssertion( "down regulation of translation initiation in response to osmotic stress") +AnnotationAssertion( "down-regulation of translation initiation in response to osmotic stress") +AnnotationAssertion( "downregulation of translation initiation in response to osmotic stress") +AnnotationAssertion( "inhibition of translation initiation in response to osmotic stress") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032063") +AnnotationAssertion(rdfs:label "negative regulation of translational initiation in response to osmotic stress") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (positive regulation of translational initiation in response to osmotic stress) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of translation initiation, as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.") +AnnotationAssertion( "up regulation of translation initiation in response to osmotic stress") +AnnotationAssertion( "up-regulation of translation initiation in response to osmotic stress") +AnnotationAssertion( "upregulation of translation initiation in response to osmotic stress") +AnnotationAssertion( "activation of translation initiation in response to osmotic stress") +AnnotationAssertion( "stimulation of translation initiation in response to osmotic stress") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032064") +AnnotationAssertion(rdfs:label "positive regulation of translational initiation in response to osmotic stress") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + # Class: (maintenance of protein location in cell cortex) AnnotationAssertion(Annotation( "GOC:vw") "A process in which a protein or protein complex is maintained in a specific location in the cell cortex.") @@ -26151,7 +26188,6 @@ SubClassOf( (stereocilium) AnnotationAssertion(Annotation( "GOC:ecd") Annotation( "PMID:15661519") Annotation( "PMID:7840137") "An actin-based protrusion from the apical surface of auditory and vestibular hair cells and of neuromast cells. These protrusions are supported by a bundle of cross-linked actin filaments (an actin cable), oriented such that the plus (barbed) ends are at the tip of the protrusion, capped by a tip complex which bridges to the plasma. Bundles of stereocilia act as mechanosensory organelles.") -AnnotationAssertion( ) AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0032420") AnnotationAssertion(rdfs:label "stereocilium") @@ -26331,10 +26367,6 @@ SubClassOf( ObjectSomeValuesFrom( "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( ) -AnnotationAssertion( ) AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T16:07:47Z") AnnotationAssertion( "GO:0044707") @@ -26989,6 +27021,23 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing complex disassembly) + +AnnotationAssertion(Annotation( "GOC:mah") "The disaggregation of a protein-containing macromolecular complex into its constituent components.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22580"^^xsd:anyURI) +AnnotationAssertion( "GO:0034623") +AnnotationAssertion( "GO:0043241") +AnnotationAssertion( "GO:0043624") +AnnotationAssertion( "protein complex disassembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "cellular macromolecule complex disassembly") +AnnotationAssertion( "cellular protein complex disassembly") +AnnotationAssertion( "macromolecule complex disassembly") +AnnotationAssertion( "GO:0032984") +AnnotationAssertion(rdfs:label "protein-containing complex disassembly") +SubClassOf( ) +SubClassOf( ) + # Class: (cellular anatomical entity morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:tb") "The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system.") @@ -27422,44 +27471,6 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (regulation of amine metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines.") -AnnotationAssertion( "regulation of amine metabolism") -AnnotationAssertion( "regulation of cellular amine metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0033238") -AnnotationAssertion(rdfs:label "regulation of amine metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (negative regulation of amine metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines.") -AnnotationAssertion( "negative regulation of amine metabolism") -AnnotationAssertion( "negative regulation of cellular amine metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0033239") -AnnotationAssertion(rdfs:label "negative regulation of amine metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (positive regulation of amine metabolic process) - -AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines.") -AnnotationAssertion( "positive regulation of amine metabolism") -AnnotationAssertion( "positive regulation of cellular amine metabolic process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0033240") -AnnotationAssertion(rdfs:label "positive regulation of amine metabolic process") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (nuclear DNA replication) AnnotationAssertion(Annotation( "GOC:mtg_cell_cycle") "The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle.") @@ -27906,6 +27917,24 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (heterochromatin boundary formation) + +AnnotationAssertion(Annotation( "GOC:mah") "A process that forms a boundary that limits the spreading of heterochromatin along a chromosome.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22028"^^xsd:anyURI) +AnnotationAssertion( "GO:0031454") +AnnotationAssertion( "regulation of extent of heterochromatin formation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "maintenance of heterochromatin boundaries") +AnnotationAssertion( "negative regulation of extent of heterochromatin assembly") +AnnotationAssertion( "negative regulation of extent of heterochromatin formation") +AnnotationAssertion( "negative regulation of heterochromatin spreading") +AnnotationAssertion( "regulation of extent of heterochromatin assembly") +AnnotationAssertion( "regulation of heterochromatin spreading") +AnnotationAssertion( "GO:0033696") +AnnotationAssertion(rdfs:label "heterochromatin boundary formation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of NAD(P)H oxidase activity) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the activity of the enzyme NAD(P)H oxidase.") @@ -29021,9 +29050,6 @@ SubClassOf( (glomerular endothelium fenestra) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "MP:0011454") Annotation( "PMID:19129259") "A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "bf") AnnotationAssertion( "2011-12-12T10:53:24Z") AnnotationAssertion(Annotation( "PMID:19129259") "GEnC fenestration") @@ -29216,6 +29242,7 @@ AnnotationAssertion( "2011-08-01T02:50:45Z") AnnotationAssertion( "receptor activity") AnnotationAssertion(Annotation( "GOC:signaling") "transport receptor activity") +AnnotationAssertion(Annotation(rdfs:label "eNOS:Caveolin-1 complex binds to Nostrin") "Reactome:R-HSA-203716") AnnotationAssertion(Annotation(rdfs:label "CUBN:AMN binds CBLIF:RCbl") "Reactome:R-HSA-3000103") AnnotationAssertion(Annotation(rdfs:label "CD320-mediated TCN2:RCbl uptake and delivery to lysosome") "Reactome:R-HSA-3000112") AnnotationAssertion(Annotation(rdfs:label "CD320 binds extracellular TCN2:RCbl") "Reactome:R-HSA-3000122") @@ -29265,7 +29292,6 @@ SubClassOf( ObjectSomeValuesFrom( (locomotion) AnnotationAssertion(Annotation( "GOC:dgh") "Self-propelled movement of a cell or organism from one location to another.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0040011") AnnotationAssertion( ) @@ -29533,7 +29559,6 @@ SubClassOf( (regulation of cell population proliferation) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of cell proliferation.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "regulation of cell proliferation") AnnotationAssertion( "GO:0042127") @@ -29575,16 +29600,16 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (cellular ketone metabolic process) +# Class: (ketone metabolic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0787650153") "The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "ketone metabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042180") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular ketone metabolic process") -SubClassOf( ) -SubClassOf( ) +AnnotationAssertion(rdfs:label "ketone metabolic process") +SubClassOf( ) # Class: (chlorinated hydrocarbon metabolic process) @@ -29603,6 +29628,7 @@ AnnotationAssertion( "GO:0042197") AnnotationAssertion(rdfs:label "halogenated hydrocarbon metabolic process") SubClassOf( ) +SubClassOf( ) # Class: (response to chemical) @@ -29625,7 +29651,6 @@ SubClassOf( (tissue regeneration) AnnotationAssertion(Annotation( "GOC:curators") "The regrowth of lost or destroyed tissues.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042246") AnnotationAssertion(rdfs:label "tissue regeneration") @@ -29840,7 +29865,6 @@ SubClassOf( "GOC:jl") "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23965"^^xsd:anyURI) -AnnotationAssertion( ) AnnotationAssertion( "GO:0034754") AnnotationAssertion( "hormone metabolism") AnnotationAssertion( "biological_process") @@ -29854,8 +29878,6 @@ SubClassOf( (melanosome) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "PMID:11584301") "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Melanosome") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0042470") @@ -29909,7 +29931,6 @@ SubClassOf( (odontogenesis) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mah") "The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.") -AnnotationAssertion( ) AnnotationAssertion( "GO:0042477") AnnotationAssertion( "Wikipedia:Odontogenesis") AnnotationAssertion( "odontogeny") @@ -30222,6 +30243,7 @@ AnnotationAssertion( "Reactome:R-HSA-1467457") AnnotationAssertion(Annotation(rdfs:label "abacavir [cytosol] + ATP + H2O => abacavir[extracellular] + ADP + phosphate") "Reactome:R-HSA-2161506") AnnotationAssertion(Annotation(rdfs:label "abacavir [cytosol] + ATP + H2O => abacavir[extracellular] + ADP + phosphate") "Reactome:R-HSA-2161538") +AnnotationAssertion(Annotation(rdfs:label "Peroxisomal uptake of very long-chain fatty acyl CoA") "Reactome:R-HSA-390393") AnnotationAssertion(Annotation(rdfs:label "PEX1:PEX6:PEX26:ZFAND6 dissociates Ub:PEX5L and PEX7 from PEX14:PEX13:PEX2:PEX10:PEX12 and translocates PEX5L and PEX7 from the peroxisomal membrane to the cytosol") "Reactome:R-HSA-9033499") AnnotationAssertion(Annotation(rdfs:label "PEX1:PEX6:PEX26:ZFAND6:Ub:PEX5S,L:PEX14:PEX13:PEX2:PEX10:PEX12 dissociates yielding cytosolic Ub:PEX5S,L and membrane PEX14:PEX13:PEX2:PEX10:PEX12") "Reactome:R-HSA-9033505") AnnotationAssertion(Annotation(rdfs:label "ABCB1 transports xenobiotics out of the cell") "Reactome:R-HSA-9659680") @@ -30270,7 +30292,6 @@ SubClassOf( ObjectSomeValuesFrom( (cholesterol homeostasis) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.") -AnnotationAssertion( ) AnnotationAssertion( "GO:2000188") AnnotationAssertion( "GO:2000189") AnnotationAssertion( "biological_process") @@ -30283,7 +30304,6 @@ SubClassOf( (hair cycle) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "PMID:12230507") "The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0042633") AnnotationAssertion(rdfs:label "hair cycle") @@ -30636,7 +30656,6 @@ SubClassOf( (regulation of apoptotic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mtg_apoptosis") "Any process that modulates the occurrence or rate of cell death by apoptotic process.") -AnnotationAssertion( ) AnnotationAssertion( "regulation of apoptosis") AnnotationAssertion( "biological_process") AnnotationAssertion( "apoptosis regulator activity") @@ -30668,7 +30687,6 @@ SubClassOf( (neuron projection) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "PMID:3077060") "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.") -AnnotationAssertion( ) AnnotationAssertion( "NIF_Subcellular:sao867568886") AnnotationAssertion( "neuron process") AnnotationAssertion(Annotation( "NIF_Subcellular:sao250931889") "neuron protrusion") @@ -30692,7 +30710,6 @@ SubClassOf( (camera-type eye development) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:mtg_sensu") "The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.") -AnnotationAssertion( ) AnnotationAssertion( "GO:0001747") AnnotationAssertion( "GO:0031075") AnnotationAssertion( "biological_process") @@ -30791,7 +30808,6 @@ 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") @@ -31055,19 +31071,22 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (non-membrane-bounded organelle) +# Class: (membraneless organelle) AnnotationAssertion(Annotation( "GOC:go_curators") "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21881"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28153"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29106"^^xsd:anyURI) AnnotationAssertion( "NIF_Subcellular:sao1456184038") +AnnotationAssertion( "membrane-less organelle") +AnnotationAssertion( "non-membrane-bounded organelle") AnnotationAssertion( "non-membrane-enclosed organelle") AnnotationAssertion( "cellular_component") AnnotationAssertion( "biological condensate") AnnotationAssertion( "GO:0043228") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "non-membrane-bounded organelle") +AnnotationAssertion(rdfs:label "membraneless organelle") SubClassOf( ) # Class: (intracellular organelle) @@ -31106,14 +31125,16 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) -# Class: (intracellular non-membrane-bounded organelle) +# Class: (intracellular membraneless organelle) AnnotationAssertion(Annotation( "GOC:go_curators") "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29106"^^xsd:anyURI) +AnnotationAssertion( "intracellular non-membrane-bounded organelle") AnnotationAssertion( "intracellular non-membrane-enclosed organelle") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0043232") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "intracellular non-membrane-bounded organelle") +AnnotationAssertion(rdfs:label "intracellular membraneless organelle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -31129,6 +31150,50 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of protein-containing complex disassembly) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.") +AnnotationAssertion( "down regulation of protein complex disassembly") +AnnotationAssertion( "down-regulation of protein complex disassembly") +AnnotationAssertion( "downregulation of protein complex disassembly") +AnnotationAssertion( "inhibition of protein complex disassembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "negative regulation of protein complex disassembly") +AnnotationAssertion( "GO:0043242") +AnnotationAssertion(rdfs:label "negative regulation of protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of protein-containing complex disassembly) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.") +AnnotationAssertion( "up regulation of protein complex disassembly") +AnnotationAssertion( "up-regulation of protein complex disassembly") +AnnotationAssertion( "upregulation of protein complex disassembly") +AnnotationAssertion( "activation of protein complex disassembly") +AnnotationAssertion( "stimulation of protein complex disassembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "positive regulation of protein complex disassembly") +AnnotationAssertion( "GO:0043243") +AnnotationAssertion(rdfs:label "positive regulation of protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (regulation of protein-containing complex disassembly) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "regulation of protein complex disassembly") +AnnotationAssertion( "GO:0043244") +AnnotationAssertion(rdfs:label "regulation of protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of protein-containing complex assembly) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of protein complex assembly.") @@ -31156,13 +31221,15 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (extracellular non-membrane-bounded organelle) +# Class: (extracellular membraneless organelle) AnnotationAssertion(Annotation( "GOC:jl") "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29106"^^xsd:anyURI) +AnnotationAssertion( "extracellular non-membrane-bounded organelle") AnnotationAssertion( "extracellular non-membrane-enclosed organelle") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0043264") -AnnotationAssertion(rdfs:label "extracellular non-membrane-bounded organelle") +AnnotationAssertion(rdfs:label "extracellular membraneless organelle") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -31848,7 +31915,7 @@ AnnotationAssertion( "GO:0043467") AnnotationAssertion(rdfs:label "regulation of generation of precursor metabolites and energy") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of carbohydrate catabolic process) @@ -32052,6 +32119,27 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of translational initiation in response to stress) + +AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of translation initiation, as a result of a stimulus indicating the organism is under stress.") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:hjd") Annotation( "GOC:tb") "regulation of translation initiation in response to stress") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0043558") +AnnotationAssertion(rdfs:label "regulation of translational initiation in response to stress") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (regulation of translational initiation in response to osmotic stress) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of translation initiation, as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0043561") +AnnotationAssertion(rdfs:label "regulation of translational initiation in response to osmotic stress") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + # Class: (regulation of respiratory gaseous exchange) AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment.") @@ -32074,8 +32162,6 @@ SubClassOf( (skin development) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "UBERON:0002097") "The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "animal skin development") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043588") @@ -32099,7 +32185,6 @@ SubClassOf( (keratinocyte proliferation) AnnotationAssertion(Annotation( "CL:0000311") "The multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population. Keratinocytes are epidermal cells which synthesize keratin and undergo a characteristic change as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043616") AnnotationAssertion(rdfs:label "keratinocyte proliferation") @@ -32362,19 +32447,6 @@ AnnotationAssertion(rdfs:label "juxt SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (cellular metabolic process) - -AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways by which individual cells transform chemical substances.") -AnnotationAssertion( "cellular metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:mah") "intermediary metabolism") -AnnotationAssertion( "GO:0044237") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") -AnnotationAssertion(rdfs:label "cellular metabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (primary metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.") @@ -32399,19 +32471,6 @@ AnnotationAssertion( "lipid digestion") SubClassOf( ) -# Class: (cellular lipid catabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the breakdown of lipids, as carried out by individual cells.") -AnnotationAssertion( "cellular lipid breakdown") -AnnotationAssertion( "cellular lipid catabolism") -AnnotationAssertion( "cellular lipid degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044242") -AnnotationAssertion(rdfs:label "cellular lipid catabolic process") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ) - # Class: (cellular catabolic process) AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.") @@ -32422,34 +32481,6 @@ AnnotationAssertion( "GO:0044248") AnnotationAssertion(rdfs:label "cellular catabolic process") SubClassOf( ) -SubClassOf( ) - -# Class: (cellular biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27052"^^xsd:anyURI) -AnnotationAssertion( "cellular anabolism") -AnnotationAssertion( "cellular biosynthesis") -AnnotationAssertion( "cellular formation") -AnnotationAssertion( "cellular synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044249") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") -AnnotationAssertion(rdfs:label "cellular biosynthetic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (cellular lipid metabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways involving lipids, as carried out by individual cells.") -AnnotationAssertion( "cellular lipid metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0044255") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular lipid metabolic process") -SubClassOf( ) -SubClassOf( ) # Class: (small molecule metabolic process) @@ -32574,7 +32605,6 @@ SubClassOf( "GOC:cc") "Any process evolved to enable an interaction with an organism of a different species.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20191"^^xsd:anyURI) -AnnotationAssertion( ) AnnotationAssertion( "interaction with another species") AnnotationAssertion( "interspecies interaction") AnnotationAssertion( "interspecies interaction between organisms") @@ -32837,9 +32867,6 @@ SubClassOf( ObjectSomeValuesFrom( (innate immune response) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:ebc") Annotation( "GOC:mtg_sensu") Annotation( "GO_REF:0000022") "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "GO:0002226") AnnotationAssertion( "Wikipedia:Innate_immune_system") AnnotationAssertion(Annotation( "GOC:pg") "innate immunity") @@ -34442,7 +34469,7 @@ AnnotationAssertion( "negative regulation of gluconeogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -34460,8 +34487,8 @@ AnnotationAssertion( "positive regulation of gluconeogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of translation) @@ -34499,7 +34526,6 @@ AnnotationAssertion( "negative regulation of DNA repair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -34517,7 +34543,6 @@ AnnotationAssertion( "positive regulation of DNA repair") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -34569,9 +34594,10 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (negative regulation of cellular amino acid metabolic process) +# Class: (negative regulation of amino acid metabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion( "down regulation of amino acid metabolic process") AnnotationAssertion( "down-regulation of amino acid metabolic process") AnnotationAssertion( "downregulation of amino acid metabolic process") @@ -34579,10 +34605,10 @@ AnnotationAssertion( "inhibition of amino acid metabolic process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0045763") -AnnotationAssertion(rdfs:label "negative regulation of cellular amino acid metabolic process") +AnnotationAssertion(rdfs:label "negative regulation of amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of amino acid metabolic process) @@ -34600,7 +34626,7 @@ AnnotationAssertion( "positive regulation of amino acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of angiogenesis) @@ -34861,6 +34887,7 @@ SubClassOf( (negative regulation of glycogen catabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29024"^^xsd:anyURI) AnnotationAssertion( "down regulation of glycogen catabolic process") AnnotationAssertion( "down-regulation of glycogen catabolic process") AnnotationAssertion( "downregulation of glycogen catabolic process") @@ -34874,13 +34901,14 @@ AnnotationAssertion( "negative regulation of glycogen catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (positive regulation of glycogen catabolic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29024"^^xsd:anyURI) AnnotationAssertion( "positive regulation of glycogen breakdown") AnnotationAssertion( "positive regulation of glycogen catabolism") AnnotationAssertion( "positive regulation of glycogen degradation") @@ -34895,7 +34923,7 @@ AnnotationAssertion( "positive regulation of glycogen catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -34919,6 +34947,7 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of glycolytic process) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of glycolysis.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29024"^^xsd:anyURI) AnnotationAssertion( "up regulation of glycolysis") AnnotationAssertion( "up-regulation of glycolysis") AnnotationAssertion( "upregulation of glycolysis") @@ -34929,7 +34958,6 @@ AnnotationAssertion( "positive regulation of glycolytic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -34999,7 +35027,6 @@ AnnotationAssertion( "negative regulation of isoprenoid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -35017,7 +35044,6 @@ AnnotationAssertion( "positive regulation of isoprenoid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -35297,6 +35323,39 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of translational termination) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination.") +AnnotationAssertion( "down regulation of translational termination") +AnnotationAssertion( "down-regulation of translational termination") +AnnotationAssertion( "downregulation of translational termination") +AnnotationAssertion( "inhibition of translational termination") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045904") +AnnotationAssertion(rdfs:label "negative regulation of translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translational termination) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of translational termination.") +AnnotationAssertion( "up regulation of translational termination") +AnnotationAssertion( "up-regulation of translational termination") +AnnotationAssertion( "upregulation of translational termination") +AnnotationAssertion( "activation of translational termination") +AnnotationAssertion( "stimulation of translational termination") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045905") +AnnotationAssertion(rdfs:label "positive regulation of translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (negative regulation of vasoconstriction) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of vasoconstriction.") @@ -35471,7 +35530,6 @@ AnnotationAssertion( "negative regulation of fatty acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -35490,7 +35548,6 @@ AnnotationAssertion( "positive regulation of fatty acid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -35693,6 +35750,37 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of translational initiation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.") +AnnotationAssertion( "down regulation of translational initiation") +AnnotationAssertion( "down-regulation of translational initiation") +AnnotationAssertion( "downregulation of translational initiation") +AnnotationAssertion( "inhibition of translational initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045947") +AnnotationAssertion(rdfs:label "negative regulation of translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of translational initiation) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of translational initiation.") +AnnotationAssertion( "up regulation of translational initiation") +AnnotationAssertion( "up-regulation of translational initiation") +AnnotationAssertion( "upregulation of translational initiation") +AnnotationAssertion( "activation of translational initiation") +AnnotationAssertion( "stimulation of translational initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045948") +AnnotationAssertion(rdfs:label "positive regulation of translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (negative regulation of natural killer cell mediated cytotoxicity) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") "Any process that stops, prevents, or reduces the rate of natural killer mediated cytotoxicity.") @@ -35740,6 +35828,37 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (negative regulation of calcium ion-dependent exocytosis) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of calcium ion-dependent exocytosis.") +AnnotationAssertion( "down regulation of calcium ion-dependent exocytosis") +AnnotationAssertion( "down-regulation of calcium ion-dependent exocytosis") +AnnotationAssertion( "downregulation of calcium ion-dependent exocytosis") +AnnotationAssertion( "inhibition of calcium ion-dependent exocytosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045955") +AnnotationAssertion(rdfs:label "negative regulation of calcium ion-dependent exocytosis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of calcium ion-dependent exocytosis) + +AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that activates or increases the frequency, rate or extent of calcium ion-dependent exocytosis.") +AnnotationAssertion( "up regulation of calcium ion-dependent exocytosis") +AnnotationAssertion( "up-regulation of calcium ion-dependent exocytosis") +AnnotationAssertion( "upregulation of calcium ion-dependent exocytosis") +AnnotationAssertion( "activation of calcium ion-dependent exocytosis") +AnnotationAssertion( "stimulation of calcium ion-dependent exocytosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0045956") +AnnotationAssertion(rdfs:label "positive regulation of calcium ion-dependent exocytosis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (negative regulation of complement activation, alternative pathway) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the alternative pathway.") @@ -36247,6 +36366,7 @@ SubClassOf( (membrane lipid catabolic process) AnnotationAssertion(Annotation( "GOC:ai") "The chemical reactions and pathways resulting in the breakdown of membrane lipids, any lipid found in or associated with a biological membrane.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:tb") "membrane lipid peroxidation") AnnotationAssertion( "membrane lipid breakdown") AnnotationAssertion( "membrane lipid catabolism") @@ -36255,7 +36375,7 @@ AnnotationAssertion( "GO:0046466") AnnotationAssertion(rdfs:label "membrane lipid catabolic process") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (nicotinamide nucleotide metabolic process) @@ -36893,17 +37013,6 @@ AnnotationAssertion(rdfs:label "carb SubClassOf( ) SubClassOf( ) -# Class: (cellular ketone body metabolic process) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism.") -AnnotationAssertion( "cellular ketone body metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0046950") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular ketone body metabolic process") -SubClassOf( ) -SubClassOf( ) - # Class: (ketone body biosynthetic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetate and acetyl-CoA.") @@ -36914,9 +37023,7 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0046951") AnnotationAssertion(rdfs:label "ketone body biosynthetic process") -SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -38623,7 +38730,6 @@ SubClassOf( ObjectSomeValuesFrom( (stem cell differentiation) AnnotationAssertion(Annotation( "CL:0000034") Annotation( "GOC:isa_complete") "The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.") -AnnotationAssertion( ) AnnotationAssertion( "Wikipedia:Stem_cell_differentiation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048863") @@ -38652,7 +38758,6 @@ SubClassOf( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:mlg") "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19809"^^xsd:anyURI) -AnnotationAssertion( ) AnnotationAssertion( "cell locomotion") AnnotationAssertion( "movement of a cell") AnnotationAssertion( "biological_process") @@ -39025,7 +39130,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of phagocytosis) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of phagocytosis, the process in which phagocytes engulf external particulate material.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0050764") AnnotationAssertion(rdfs:label "regulation of phagocytosis") @@ -39497,7 +39601,6 @@ SubClassOf( ObjectSomeValuesFrom( (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") @@ -39579,8 +39682,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of T cell activation) AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of T cell activation.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "positive regulation of T lymphocyte activation") AnnotationAssertion( "positive regulation of T-cell activation") AnnotationAssertion( "positive regulation of T-lymphocyte activation") @@ -39630,7 +39731,6 @@ SubClassOf( (brown fat cell differentiation) AnnotationAssertion(Annotation( "PMID:12588810") "The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.") -AnnotationAssertion( ) AnnotationAssertion( "brown adipocyte cell differentiation") AnnotationAssertion( "brown adipocyte differentiation") AnnotationAssertion( "biological_process") @@ -40562,7 +40662,7 @@ AnnotationAssertion( "GO:0051174") AnnotationAssertion(rdfs:label "regulation of phosphorus metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (localization) @@ -41542,7 +41642,6 @@ SubClassOf( ObjectSomeValuesFrom( (keratinocyte migration) AnnotationAssertion(Annotation( "ISBN:0721662544") "The directed movement of a keratinocyte, epidermal cells which synthesize keratin, from one site to another.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051546") AnnotationAssertion(rdfs:label "keratinocyte migration") @@ -43213,7 +43312,6 @@ SubClassOf( ObjectSomeValuesFrom( (urinary bladder development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:ln") Annotation( "GOC:mr") Annotation( "PMID:11768524") Annotation( "PMID:18276178") Annotation( "PMID:538956") "The process whose specific outcome is the progression of the urinary bladder over time, from its formation to the mature structure. The urinary bladder is an elastic, muscular sac situated in the anterior part of the pelvic cavity in which urine collects before excretion.") -AnnotationAssertion( ) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060157") AnnotationAssertion(rdfs:label "urinary bladder development") @@ -44046,6 +44144,17 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (acrosomal vesicle exocytosis) + +AnnotationAssertion(Annotation( "GOC:dph") "The calcium ion regulated exocytosis which results in fusion of the acrosomal vesicle with the plasma membrane of the sperm as part of the acrosome reaction.") +AnnotationAssertion(Annotation( "GOC:dph") "acrosome exocytosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") "acrosomal granule exocytosis") +AnnotationAssertion( "GO:0060478") +AnnotationAssertion(rdfs:label "acrosomal vesicle exocytosis") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (lung-associated mesenchyme development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_lung") "The biological process whose specific outcome is the progression of a lung-associated mesenchyme from an initial condition to its mature state. This process begins with the formation of lung-associated mesenchyme and ends with the mature structure. Lung-associated mesenchyme is the tissue made up of loosely connected mesenchymal cells in the lung.") @@ -44067,6 +44176,18 @@ AnnotationAssertion(rdfs:label "mese SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of cell projection assembly) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of cell projection assembly.") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "regulation of cell projection formation") +AnnotationAssertion( "GO:0060491") +AnnotationAssertion(rdfs:label "regulation of cell projection assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (cell-cell signaling involved in lung development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_lung") "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the lung, from its initial state to the mature structure.") @@ -44123,7 +44244,6 @@ SubClassOf( (diaphragm development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs.") -AnnotationAssertion( ) AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T08:44:56Z") AnnotationAssertion( "biological_process") @@ -44662,7 +44782,6 @@ AnnotationAssertion( "GO:0060696") AnnotationAssertion(rdfs:label "regulation of phospholipid catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -44676,7 +44795,6 @@ AnnotationAssertion( "GO:0060697") AnnotationAssertion(rdfs:label "positive regulation of phospholipid catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -46324,6 +46442,18 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (mitochondrial translational initiation) + +AnnotationAssertion(Annotation( "GOC:mah") "The process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA.") +AnnotationAssertion(Annotation( "GOC:mah") "mitochondrial translation initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0070124") +AnnotationAssertion(rdfs:label "mitochondrial translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (mitochondrial translational elongation) AnnotationAssertion(Annotation( "GOC:mah") "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in a mitochondrion.") @@ -46336,6 +46466,18 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (mitochondrial translational termination) + +AnnotationAssertion(Annotation( "GOC:mah") Annotation( "http://mitogenome.org/index.php/Genetic_Code_of_mitochondria") "The process resulting in the release of a polypeptide chain from the ribosome in a mitochondrion, usually in response to a termination codon (note that mitochondria use variants of the universal genetic code that differ between different taxa).") +AnnotationAssertion(Annotation( "GOC:mah") "mitochondrial translation termination") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0070126") +AnnotationAssertion(rdfs:label "mitochondrial translational termination") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of mitochondrial translation) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion.") @@ -46381,6 +46523,43 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of mitochondrial translational initiation) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion.") +AnnotationAssertion(Annotation( "GOC:mah") "regulation of mitochondrial translation initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0070132") +AnnotationAssertion(rdfs:label "regulation of mitochondrial translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of mitochondrial translational initiation) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion.") +AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of mitochondrial translation initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0070133") +AnnotationAssertion(rdfs:label "negative regulation of mitochondrial translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of mitochondrial translational initiation) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion.") +AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of mitochondrial translation initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0070134") +AnnotationAssertion(rdfs:label "positive regulation of mitochondrial translational initiation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (tight junction) AnnotationAssertion(Annotation( "ISBN:0815332181") "A cell-cell junction that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other.") @@ -47099,6 +47278,18 @@ AnnotationAssertion(rdfs:label "inte SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (heterochromatin organization) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26702"^^xsd:anyURI) +AnnotationAssertion( "mah") +AnnotationAssertion( "2009-07-23T04:12:48Z") +AnnotationAssertion(Annotation( "GOC:mah") "heterochromatin organisation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0070828") +AnnotationAssertion(rdfs:label "heterochromatin organization") +SubClassOf( ) + # Class: (regulation of glycogen metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen.") @@ -47124,7 +47315,6 @@ AnnotationAssertion( "negative regulation of glycogen metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -47141,7 +47331,6 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -47715,6 +47904,21 @@ SubClassOf( ) SubClassOf( ) +# Class: (protein-RNA complex organization) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25143"^^xsd:anyURI) +AnnotationAssertion( "mah") +AnnotationAssertion( "2010-09-08T10:10:35Z") +AnnotationAssertion(Annotation( "GOC:mah") "RNA-protein complex subunit organization") +AnnotationAssertion(Annotation( "GOC:mah") "protein-RNA complex subunit organization") +AnnotationAssertion(Annotation( "GOC:mah") "ribonucleoprotein complex subunit organisation") +AnnotationAssertion( "ribonucleoprotein complex subunit organization") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0071826") +AnnotationAssertion(rdfs:label "protein-RNA complex organization") +SubClassOf( ) + # Class: (cellular component organization or biogenesis) AnnotationAssertion(Annotation( "GOC:mah") "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.") @@ -49702,6 +49906,44 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (organohalogen metabolic process) + +AnnotationAssertion(Annotation( "GOC:BHF") "The chemical reactions and pathways involving organohalogen compounds, as carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) +AnnotationAssertion( "tb") +AnnotationAssertion( "2010-06-02T10:36:42Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0090345") +AnnotationAssertion(rdfs:label "organohalogen metabolic process") +SubClassOf( ) + +# Class: (regulation of organohalogen metabolic process) + +AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways involving organohalogen compounds, as carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) +AnnotationAssertion( "tb") +AnnotationAssertion( "2010-06-02T10:36:42Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0090347") +AnnotationAssertion(rdfs:label "regulation of organohalogen metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of organohalogen metabolic process) + +AnnotationAssertion(Annotation( "GOC:BHF") "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways involving organohalogen compounds, as carried out by individual cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) +AnnotationAssertion( "tb") +AnnotationAssertion( "2010-06-02T10:36:42Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0090349") +AnnotationAssertion(rdfs:label "negative regulation of organohalogen metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of ornithine metabolic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jp") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.") @@ -49712,6 +49954,7 @@ AnnotationAssertion( "regulation of ornithine metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of cholesterol efflux) @@ -49736,7 +49979,7 @@ AnnotationAssertion( AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090399") AnnotationAssertion(rdfs:label "replicative senescence") -SubClassOf( ) +SubClassOf( ) # Class: (organophosphate biosynthetic process) @@ -49959,6 +50202,35 @@ AnnotationAssertion(rdfs:label "dent SubClassOf( ) SubClassOf( ) +# Class: (apoptotic signaling pathway) + +AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2011-11-23T09:30:23Z") +AnnotationAssertion( "GO:0008624") +AnnotationAssertion(Annotation( "GOC:mah") "apoptotic signalling pathway") +AnnotationAssertion( "induction of apoptosis by extracellular signals") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0097190") +AnnotationAssertion(rdfs:comment "This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways.") +AnnotationAssertion(rdfs:label "apoptotic signaling pathway") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (execution phase of apoptosis) + +AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:21760595") "A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2011-11-23T09:45:24Z") +AnnotationAssertion( "execution phase of apoptotic process") +AnnotationAssertion( "apoptosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0097194") +AnnotationAssertion(rdfs:label "execution phase of apoptosis") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (renal filtration) AnnotationAssertion(Annotation( "GOC:pr") Annotation( "GOC:sart") "A renal system process in which fluid circulating through the body is filtered through a barrier system.") @@ -50096,7 +50368,6 @@ SubClassOf( (keratinocyte apoptotic process) AnnotationAssertion(Annotation( "CL:0000312") Annotation( "GOC:jc") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:10201527") "Any apoptotic process in a keratinocyte. A keratinocyte is an epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin.") -AnnotationAssertion( ) AnnotationAssertion( "pr") AnnotationAssertion( "2012-03-29T10:20:51Z") AnnotationAssertion( "keratinocyte apoptosis") @@ -51538,18 +51809,20 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (cellular anatomical entity) +# Class: (cellular anatomical structure) -AnnotationAssertion(Annotation( "GOC:kmv") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion(Annotation( "GOC:kmv") "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24200"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28978"^^xsd:anyURI) AnnotationAssertion( "kmv") AnnotationAssertion( "2019-08-12T18:01:37Z") +AnnotationAssertion( "cellular anatomical entity") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0110165") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "cellular anatomical entity") +AnnotationAssertion(rdfs:label "cellular anatomical structure") SubClassOf( ) # Class: (DNA synthesis involved in mitochondrial DNA replication) @@ -51580,6 +51853,62 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (plasma membrane bounded cell projection assembly) + +AnnotationAssertion(Annotation( "GOC:krc") "Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) +AnnotationAssertion( "krc") +AnnotationAssertion( "2017-04-24T23:56:08Z") +AnnotationAssertion(Annotation( "GOC:krc") Annotation( "GOC:rjd") Annotation( "PMID:10328951") Annotation( "PMID:9096956") "eupodium") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0120031") +AnnotationAssertion(rdfs:label "plasma membrane bounded cell projection assembly") +SubClassOf( ) +SubClassOf( ) + +# Class: (regulation of plasma membrane bounded cell projection assembly) + +AnnotationAssertion(Annotation( "GOC:krc") "Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) +AnnotationAssertion( "krc") +AnnotationAssertion( "2017-04-26T04:27:04Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0120032") +AnnotationAssertion(rdfs:label "regulation of plasma membrane bounded cell projection assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of plasma membrane bounded cell projection assembly) + +AnnotationAssertion(Annotation( "GOC:krc") "Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) +AnnotationAssertion( "krc") +AnnotationAssertion( "2017-04-26T04:34:31Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0120033") +AnnotationAssertion(rdfs:label "negative regulation of plasma membrane bounded cell projection assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of plasma membrane bounded cell projection assembly) + +AnnotationAssertion(Annotation( "GOC:krc") "Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) +AnnotationAssertion( "krc") +AnnotationAssertion( "2017-04-26T04:34:45Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0120034") +AnnotationAssertion(rdfs:label "positive regulation of plasma membrane bounded cell projection assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of plasma membrane bounded cell projection organization) AnnotationAssertion(Annotation( "GOC:krc") "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections.") @@ -51794,6 +52123,56 @@ AnnotationAssertion( "olefinic compound metabolic process") SubClassOf( ) +# Class: (regulation of heterochromatin organization) + +AnnotationAssertion(Annotation( "GOC:krc") "Any process that modulates the frequency, rate, extent or location of heterochromatin organization.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20020"^^xsd:anyURI) +AnnotationAssertion( "krc") +AnnotationAssertion( "2020-09-29T20:00:04Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0120261") +AnnotationAssertion(rdfs:label "regulation of heterochromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of heterochromatin organization) + +AnnotationAssertion(Annotation( "GOC:krc") "Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin organization.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20020"^^xsd:anyURI) +AnnotationAssertion( "krc") +AnnotationAssertion( "2020-09-29T20:12:30Z") +AnnotationAssertion( "down regulation of heterochromatin organization") +AnnotationAssertion( "down-regulation of heterochromatin organization") +AnnotationAssertion( "downregulation of heterochromatin organization") +AnnotationAssertion( "inhibition of heterochromatin organization") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0120262") +AnnotationAssertion(rdfs:label "negative regulation of heterochromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of heterochromatin organization) + +AnnotationAssertion(Annotation( "GOC:krc") "Any process that activates or increases the frequency, rate or extent of heterochromatin organization.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20020"^^xsd:anyURI) +AnnotationAssertion( "krc") +AnnotationAssertion( "2020-09-29T20:19:19Z") +AnnotationAssertion( "up regulation of heterochromatin organization") +AnnotationAssertion( "up-regulation of heterochromatin organization") +AnnotationAssertion( "upregulation of heterochromatin organization") +AnnotationAssertion( "activation of heterochromatin organization") +AnnotationAssertion( "stimulation of heterochromatin organization") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0120263") +AnnotationAssertion(rdfs:label "positive regulation of heterochromatin organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of pigmentation) AnnotationAssertion(Annotation( "GOC:krc") "Any process that modulates the frequency, rate or extent of the deposition or modulates the distribution of coloring matter in an organism.") @@ -52233,18 +52612,20 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (non-membrane-bounded organelle assembly) +# Class: (membraneless organelle assembly) AnnotationAssertion(Annotation( "PMID:28225081") "The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21939"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29106"^^xsd:anyURI) AnnotationAssertion( "pg") AnnotationAssertion( "2021-08-09T15:30:06Z") +AnnotationAssertion( "non-membrane-bounded organelle assembly") AnnotationAssertion( "non-membrane-bounded organelle formation") AnnotationAssertion( "non-membrane-enclosed organelle assembly") AnnotationAssertion( "non-membrane-enclosed organelle formation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140694") -AnnotationAssertion(rdfs:label "non-membrane-bounded organelle assembly") +AnnotationAssertion(rdfs:label "membraneless organelle assembly") SubClassOf( ) # Class: (metal cation:monoatomic cation antiporter activity) @@ -52701,6 +53082,52 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (regulation of execution phase of apoptosis) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") "Any process that modulates the frequency, rate or extent of execution phase of apoptosis.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2012-02-22T11:26:20Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1900117") +AnnotationAssertion(rdfs:label "regulation of execution phase of apoptosis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of execution phase of apoptosis) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2012-02-22T11:26:24Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of execution phase of apoptosis") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of execution phase of apoptosis") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of execution phase of apoptosis") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of execution phase of apoptosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1900118") +AnnotationAssertion(rdfs:label "negative regulation of execution phase of apoptosis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of execution phase of apoptosis) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") "Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2012-02-22T11:26:27Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of execution phase of apoptosis") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of execution phase of apoptosis") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of execution phase of apoptosis") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of execution phase of apoptosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1900119") +AnnotationAssertion(rdfs:label "positive regulation of execution phase of apoptosis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of oligodendrocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of oligodendrocyte apoptotic process.") @@ -53613,6 +54040,64 @@ AnnotationAssertion(rdfs:label "carb SubClassOf( ) SubClassOf( ) +# Class: (regulation of formation of translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex.") +AnnotationAssertion( "ss") +AnnotationAssertion( "2012-07-25T02:26:58Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of translation initiation ternary complex assembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901190") +AnnotationAssertion(rdfs:label "regulation of formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of formation of translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex.") +AnnotationAssertion( "ss") +AnnotationAssertion( "2012-07-25T02:27:21Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of formation of translation initiation ternary complex") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901191") +AnnotationAssertion(rdfs:label "negative regulation of formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of formation of translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex.") +AnnotationAssertion( "ss") +AnnotationAssertion( "2012-07-25T02:27:29Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of formation of translation initiation ternary complex") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of translation initiation ternary complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of formation of translation initiation ternary complex") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1901192") +AnnotationAssertion(rdfs:label "positive regulation of formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of heart looping) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of heart looping.") @@ -54295,7 +54780,7 @@ AnnotationAssertion( "GO:1901856") AnnotationAssertion(rdfs:label "negative regulation of cellular respiration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -54327,7 +54812,7 @@ AnnotationAssertion( "GO:1901857") AnnotationAssertion(rdfs:label "positive regulation of cellular respiration") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -55256,6 +55741,7 @@ SubClassOf( ObjectSomeValuesFrom( (ketone body metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways involving ketone body.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22938"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2013-06-13T10:37:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "ketone body metabolism") @@ -55263,6 +55749,7 @@ AnnotationAssertion( "GO:1902224") AnnotationAssertion(rdfs:label "ketone body metabolic process") SubClassOf( ) +SubClassOf( ) SubClassOf( ) # Class: (negative regulation of acrosome reaction) @@ -59157,10 +59644,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000085") Annotation( "PMID:19137015") "Any apoptotic process in an epithelial cell.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-06T22:27:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "epitheliocyte apoptotic process") @@ -59548,6 +60031,63 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of bleb assembly) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:25651887") "Any process that modulates the frequency, rate or extent of bleb assembly.") +AnnotationAssertion( "als") +AnnotationAssertion( "2015-04-23T09:32:19Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cell blebbing") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904170") +AnnotationAssertion(rdfs:label "regulation of bleb assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of bleb assembly) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:25651887") "Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly.") +AnnotationAssertion( "als") +AnnotationAssertion( "2015-04-23T09:32:25Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of bleb assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cell blebbing") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of bleb assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cell blebbing") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of bleb assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of cell blebbing") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of cell blebbing") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of bleb assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of cell blebbing") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904171") +AnnotationAssertion(rdfs:label "negative regulation of bleb assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of bleb assembly) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:25651887") "Any process that activates or increases the frequency, rate or extent of bleb assembly.") +AnnotationAssertion( "als") +AnnotationAssertion( "2015-04-23T09:32:31Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cell blebbing") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of bleb assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cell blebbing") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of bleb assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cell blebbing") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of bleb assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of cell blebbing") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of bleb assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of cell blebbing") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904172") +AnnotationAssertion(rdfs:label "positive regulation of bleb assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of adipose tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23081848") "Any process that modulates the frequency, rate or extent of adipose tissue development.") @@ -60178,7 +60718,7 @@ AnnotationAssertion( "GO:1904726") AnnotationAssertion(rdfs:label "regulation of replicative senescence") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (negative regulation of replicative senescence) @@ -60194,7 +60734,7 @@ AnnotationAssertion( "GO:1904727") AnnotationAssertion(rdfs:label "negative regulation of replicative senescence") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -60211,7 +60751,7 @@ AnnotationAssertion( "GO:1904728") AnnotationAssertion(rdfs:label "positive regulation of replicative senescence") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -60261,6 +60801,31 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (Atg1/ULK1 kinase complex assembly) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000079") Annotation( "PMID:25139988") "The aggregation, arrangement and bonding together of a set of components to form an Atg1/UKL1 kinase complex.") +AnnotationAssertion( "dph") +AnnotationAssertion( "2015-10-19T12:33:08Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1904745") +AnnotationAssertion(rdfs:label "Atg1/ULK1 kinase complex assembly") +SubClassOf( ) + # Class: (negative regulation of apoptotic process involved in development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22801495") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development.") @@ -60933,7 +61498,6 @@ AnnotationAssertion( "regulation of membrane lipid metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of Schwann cell proliferation involved in axon regeneration) @@ -61763,7 +62327,7 @@ AnnotationAssertion( "GO:1905448") AnnotationAssertion(rdfs:label "positive regulation of mitochondrial ATP synthesis coupled electron transport") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -62413,6 +62977,217 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of Atg1/ULK1 kinase complex assembly) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:autophagy") Annotation( "GOC:mf") Annotation( "GO_REF:0000058") Annotation( "PMID:26567215") "Any process that modulates the frequency, rate or extent of Atg1/ULK1 kinase complex assembly.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2017-01-26T13:23:26Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905864") +AnnotationAssertion(rdfs:label "regulation of Atg1/ULK1 kinase complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of Atg1/ULK1 kinase complex assembly) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:autophagy") Annotation( "GOC:mf") Annotation( "GO_REF:0000058") Annotation( "PMID:26567215") "Any process that stops, prevents or reduces the frequency, rate or extent of Atg1/ULK1 kinase complex assembly.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2017-01-26T13:23:35Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1/ULK1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1/ULK1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1/ULK1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "downregulation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1/ULK1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905865") +AnnotationAssertion(rdfs:label "negative regulation of Atg1/ULK1 kinase complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of Atg1/ULK1 kinase complex assembly) + +AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:autophagy") Annotation( "GOC:mf") Annotation( "GO_REF:0000058") Annotation( "PMID:26567215") "Any process that activates or increases the frequency, rate or extent of Atg1/ULK1 kinase complex assembly.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2017-01-26T13:23:44Z") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1/ULK1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1/ULK1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1/ULK1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1-ATG13 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1-ATG13 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1/ULK1 kinase complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1/ULK1 kinase complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1/ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ATG1/ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of Atg1p signalling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of Atg1p signalling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1 signaling complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1 signaling complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1-ATG13-FIP200 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1-ATG13-FIP200 complex formation") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1-ATG13-RB1CC1 complex assembly") +AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ULK1-ATG13-RB1CC1 complex formation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:1905866") +AnnotationAssertion(rdfs:label "positive regulation of Atg1/ULK1 kinase complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of oogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26434723") "Any process that modulates the frequency, rate or extent of oogenesis.") @@ -63883,6 +64658,36 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of acrosomal vesicle exocytosis) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of acrosomal vesicle exocytosis.") +AnnotationAssertion( "yaf") +AnnotationAssertion( "2011-02-07T11:52:34Z") +AnnotationAssertion(Annotation( "GOC:obol") "regulation of acrosome exocytosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:obol") "regulation of acrosomal granule exocytosis") +AnnotationAssertion( "GO:2000367") +AnnotationAssertion(rdfs:label "regulation of acrosomal vesicle exocytosis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of acrosomal vesicle exocytosis) + +AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of acrosomal vesicle exocytosis.") +AnnotationAssertion( "yaf") +AnnotationAssertion( "2011-02-07T11:52:42Z") +AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of acrosome exocytosis") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of acrosomal granule exocytosis") +AnnotationAssertion( "GO:2000368") +AnnotationAssertion(rdfs:label "positive regulation of acrosomal vesicle exocytosis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (regulation of mesoderm development) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of mesoderm development.") @@ -65593,6 +66398,50 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (regulation of apoptotic signaling pathway) + +AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that modulates the frequency, rate or extent of apoptotic signaling pathway.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2011-11-24T01:20:49Z") +AnnotationAssertion(Annotation( "GOC:mah") "regulation of apoptotic signalling pathway") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2001233") +AnnotationAssertion(rdfs:label "regulation of apoptotic signaling pathway") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (negative regulation of apoptotic signaling pathway) + +AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2011-11-24T01:20:54Z") +AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of apoptotic signalling pathway") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2001234") +AnnotationAssertion(rdfs:label "negative regulation of apoptotic signaling pathway") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (positive regulation of apoptotic signaling pathway) + +AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.") +AnnotationAssertion( "pr") +AnnotationAssertion( "2011-11-24T01:20:58Z") +AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of apoptotic signalling pathway") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:2001235") +AnnotationAssertion(rdfs:label "positive regulation of apoptotic signaling pathway") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (negative regulation of chromosome organization) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization.") diff --git a/src/ontology/imports/mpath_import.owl b/src/ontology/imports/mpath_import.owl index d7633a8a..2b688a4e 100644 --- a/src/ontology/imports/mpath_import.owl +++ b/src/ontology/imports/mpath_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-11-11") +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/nbo_import.owl b/src/ontology/imports/nbo_import.owl index 24012755..627977b4 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 "2024-11-11") +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index b09510af..b1b89236 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 "2024-11-11") +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pr_import.owl b/src/ontology/imports/pr_import.owl index f5dc4df3..34ec8615 100644 --- a/src/ontology/imports/pr_import.owl +++ b/src/ontology/imports/pr_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-11-11") + +Annotation( ) +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class()) @@ -70,6 +70,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -129,6 +130,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -168,7 +171,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -388,11 +391,11 @@ SubClassOf( (molecular_function) -AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") +AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.") AnnotationAssertion( "molecular function") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0003674") -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") AnnotationAssertion(rdfs:label "molecular_function") # Class: (cellular_component) @@ -415,11 +418,11 @@ SubClassOf( (biological_process) -AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion(Annotation( "GOC:pdt") "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") AnnotationAssertion( "biological process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0008150") -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") AnnotationAssertion(rdfs:label "biological_process") # Class: (calcium-activated potassium channel activity) @@ -478,7 +481,7 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "protein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -585,6 +588,7 @@ SubClassOf( (interleukin-17) AnnotationAssertion(Annotation( "PMID:17982105") Annotation( "PMID:18280574") "A protein that is a T cell-derived cytokine that may play an important role in the initiation or maintenance of the proinflammatory response. Except for IL-17B, all other IL-17 family members are homodimers containing five highly conserved cysteine residues forming characteristic cystein-knot structure, similar to that found in the TGF-beta-like cystine-knot (PR:000000008). This class consists of six cytokines. Among them, interleukin 17A (IL-17) and IL-17F are expressed by a novel subset of CD4+ helper T (Th) cells and play a critical role in inflammation and autoimmunity. On the other hand, IL-17E, also called IL-25, has been associated with allergic responses.") +AnnotationAssertion( "PANTHER:PTHR21295") AnnotationAssertion( "PIRSF:PIRSF003430") AnnotationAssertion( "IL17") AnnotationAssertion(Annotation( "PRO:DAN") Annotation( ) "fam:IL-17") @@ -914,14 +918,14 @@ SubClassOf( (interleukin-10) -AnnotationAssertion(Annotation( "PRO:JAN") "A class 2 cytokine, IL-10 type that is a translation product of the human IL10 gene or a 1:1 ortholog thereof.") +AnnotationAssertion(Annotation( "PANTHER:PTHR11585:SF1") Annotation( "PRO:JAN") "A class 2 cytokine, IL-10 type that is a translation product of the human IL10 gene or a 1:1 ortholog thereof. Active interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. Structurally, IL-10 is a protein of about 160 amino acids that contains four conserved cysteines involved in disulfide bonds.") AnnotationAssertion( "CSIF") AnnotationAssertion( "IL-10") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "IL10") AnnotationAssertion( "cytokine synthesis inhibitory factor") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000001471") -AnnotationAssertion(rdfs:comment "Category=gene. Note: Active interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. Structurally, IL-10 is a protein of about 160 amino acids that contains four conserved cysteines involved in disulfide bonds.") +AnnotationAssertion(rdfs:comment "Category=gene.") AnnotationAssertion(rdfs:label "interleukin-10") AnnotationAssertion( ) SubClassOf( ) @@ -1085,6 +1089,27 @@ AnnotationAssertion(rdfs:label "C- AnnotationAssertion( ) SubClassOf( ) +# Class: (C-X-C motif chemokine 10) + +AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human CXCL10 gene or a 1:1 ortholog thereof.") +AnnotationAssertion(Annotation( "PRO:DNx") "C7") +AnnotationAssertion( "10 kDa interferon gamma-induced protein") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CXCL10") +AnnotationAssertion( "IP-10") +AnnotationAssertion( "gamma-IP10") +AnnotationAssertion( "interferon-gamma induced protein CRG-2") +AnnotationAssertion( "small-inducible cytokine B10") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( ) "Crg2") +AnnotationAssertion(Annotation( ) "INP10") +AnnotationAssertion(Annotation( ) "Ifi10") +AnnotationAssertion(Annotation( ) "SCYB10") +AnnotationAssertion( "PR:000006064") +AnnotationAssertion(rdfs:comment "Category=gene.") +AnnotationAssertion(rdfs:label "C-X-C motif chemokine 10") +AnnotationAssertion( ) +SubClassOf( ) + # Class: (elastin) AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human ELN gene or a 1:1 ortholog thereof.") @@ -1335,19 +1360,18 @@ AnnotationAssertion(rdfs:label "al AnnotationAssertion( ) SubClassOf( ) -# Class: (pancreatic polypeptide prohormone) +# Class: (pancreatic prohormone) AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human PPY gene or a 1:1 ortholog thereof.") AnnotationAssertion( "PP") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "PPY") AnnotationAssertion( "obinepitide") AnnotationAssertion( "pancreatic polypeptide") -AnnotationAssertion( "pancreatic prohormone") AnnotationAssertion( "protein") AnnotationAssertion(Annotation( ) "PNP") AnnotationAssertion( "PR:000013164") AnnotationAssertion(rdfs:comment "Category=gene.") -AnnotationAssertion(rdfs:label "pancreatic polypeptide prohormone") +AnnotationAssertion(rdfs:label "pancreatic prohormone") AnnotationAssertion( ) SubClassOf( ) @@ -1887,6 +1911,31 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (C-X-C motif chemokine 10, signal peptide removed form) + +AnnotationAssertion(Annotation( "PRO:DNx") "A C-X-C motif chemokine 10 that has had the signal peptide removed.") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CXCL10/SigPep-") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000019587") +AnnotationAssertion(rdfs:comment "Category=modification.") +AnnotationAssertion(rdfs:label "C-X-C motif chemokine 10, signal peptide removed form") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (C-X-C motif chemokine 10 proteolytic cleavage product) + +AnnotationAssertion(Annotation( "PRO:DNx") "A C-X-C motif chemokine 10 that has been processed by proteolytic cleavage.") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "CXCL10/ClvPrd") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000019588") +AnnotationAssertion(rdfs:comment "Category=modification.") +AnnotationAssertion(rdfs:label "C-X-C motif chemokine 10 proteolytic cleavage product") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (erythropoietin, signal peptide removed form) AnnotationAssertion(Annotation( "PRO:DNx") "An erythropoietin that has had the signal peptide removed.") @@ -2050,26 +2099,26 @@ EquivalentClasses( ObjectIntersecti SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (pancreatic polypeptide prohormone, signal peptide removed form) +# Class: (pancreatic prohormone, signal peptide removed form) -AnnotationAssertion(Annotation( "PRO:DNx") "A pancreatic polypeptide prohormone that has had the signal peptide removed.") +AnnotationAssertion(Annotation( "PRO:DNx") "A pancreatic prohormone that has had the signal peptide removed.") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "PPY/SigPep-") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000021065") AnnotationAssertion(rdfs:comment "Category=modification.") -AnnotationAssertion(rdfs:label "pancreatic polypeptide prohormone, signal peptide removed form") +AnnotationAssertion(rdfs:label "pancreatic prohormone, signal peptide removed form") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (pancreatic polypeptide prohormone proteolytic cleavage product) +# Class: (pancreatic prohormone proteolytic cleavage product) -AnnotationAssertion(Annotation( "PRO:DNx") "A pancreatic polypeptide prohormone that has been processed by proteolytic cleavage.") +AnnotationAssertion(Annotation( "PRO:DNx") "A pancreatic prohormone that has been processed by proteolytic cleavage.") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "PPY/ClvPrd") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000021066") AnnotationAssertion(rdfs:comment "Category=modification.") -AnnotationAssertion(rdfs:label "pancreatic polypeptide prohormone proteolytic cleavage product") +AnnotationAssertion(rdfs:label "pancreatic prohormone proteolytic cleavage product") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) @@ -2266,6 +2315,7 @@ SubClassOf( (serpin) AnnotationAssertion(Annotation( "InterPro:IPR000215") Annotation( "PRO:CNA") "A protein that is primarily known as an irreversible serine protease inhibitor active against S1, S8 and C14 peptidases. There are both extra- and intra-cellular serpins, which are found in all groups of organisms with the notable exception of fungi. Serpin contains a copy of the Serpin (Pfam:PF00079) domain.") +AnnotationAssertion( "PANTHER:PTHR11461") AnnotationAssertion( "PIRSF:PIRSF001630") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000025875") @@ -2352,20 +2402,20 @@ AnnotationAssertion(rdfs:label "al AnnotationAssertion( ) SubClassOf( ) -# Class: (protein-containing molecular entity) - -AnnotationAssertion(Annotation( "PRO:DAN") "A molecular entity that minimally consists of a protein.") -AnnotationAssertion(Annotation( "PRO:DAN") "protein") -AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") -AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") -AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") -AnnotationAssertion( "protein") -AnnotationAssertion( "PR:000064867") -AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565).") -AnnotationAssertion(rdfs:label "protein-containing molecular entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing material entity) + +AnnotationAssertion(Annotation( "PRO:DAN") "A material entity that minimally consists of a protein.") +AnnotationAssertion(Annotation( "PRO:DAN") "protein") +AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") +AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") +AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000050567") +AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).") +AnnotationAssertion(rdfs:label "protein-containing material entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sequence_feature) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 0d5944ed..ddb8fd2b 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 "2024-11-11") +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index a81609c7..7fe165f4 100644 --- a/src/ontology/imports/uberon_import.owl +++ b/src/ontology/imports/uberon_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( ) Annotation( ) @@ -68,7 +68,7 @@ Annotation( "PMID:16417468 Forgotten and Annotation( "aggregates AAO from 13:04:2012") Annotation( "aggregates TAO from 09:08:2012") Annotation( "aggregates VSAO from 16:07:2012") -Annotation(owl:versionInfo "2024-11-11") +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class()) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index c0985599..373af848 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-11-11") + +Annotation(owl:versionInfo "2024-11-12") Declaration(Class()) Declaration(Class())