diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 1221087a3..8061ad1bc 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -4258,10 +4258,9 @@ alt_id: GO:0000420 def: "RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase V, while the largest subunit is found only in RNAP IV complex." [GOC:krc, GOC:mtg_sensu, PMID:15692015, PMID:15766525, PMID:16140984, PMID:19110459] synonym: "DNA-directed RNA polymerase IV complex" EXACT [] synonym: "DNA-directed RNA polymerase IVa complex" EXACT [] +is_a: GO:0000428 ! DNA-directed RNA polymerase complex is_a: GO:0140513 ! nuclear protein-containing complex -intersection_of: GO:0000428 ! DNA-directed RNA polymerase complex -intersection_of: capable_of GO:0001057 ! RNA polymerase IV activity -intersection_of: part_of GO:0005634 ! nucleus +relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000419 @@ -4271,10 +4270,9 @@ alt_id: GO:0080137 def: "RNA polymerase V is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol V is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits." [GOC:krc, GOC:mtg_sensu, PMID:16140984, PMID:19110459] synonym: "DNA-directed RNA polymerase IVb complex" EXACT [] synonym: "DNA-directed RNA polymerase V complex" EXACT [] +is_a: GO:0000428 ! DNA-directed RNA polymerase complex is_a: GO:0140513 ! nuclear protein-containing complex -intersection_of: GO:0000428 ! DNA-directed RNA polymerase complex -intersection_of: capable_of GO:0001058 ! RNA polymerase V activity -intersection_of: part_of GO:0005634 ! nucleus +relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000421 @@ -7759,72 +7757,68 @@ name: RNA polymerase I activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase I specific promoter to direct initiation and catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase I promoter" EXACT [] -xref: EC:2.7.7.6 {source="skos:broadMatch"} intersection_of: GO:0003899 ! DNA-directed 5'-3' RNA polymerase activity intersection_of: part_of GO:0006360 ! transcription by RNA polymerase I relationship: occurs_in GO:0000785 ! chromatin relationship: part_of GO:0006360 ! transcription by RNA polymerase I +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI created_by: krc creation_date: 2010-09-23T03:36:11Z [Term] id: GO:0001055 -name: RNA polymerase II activity +name: obsolete RNA polymerase II activity namespace: molecular_function -def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity. synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase II promoter" EXACT [] -xref: EC:2.7.7.6 {source="skos:broadMatch"} -intersection_of: GO:0003899 ! DNA-directed 5'-3' RNA polymerase activity -intersection_of: part_of GO:0006366 ! transcription by RNA polymerase II -relationship: occurs_in GO:0000785 ! chromatin -relationship: part_of GO:0006366 ! transcription by RNA polymerase II +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI +is_obsolete: true +replaced_by: GO:0003899 created_by: krc creation_date: 2010-09-23T03:44:23Z [Term] id: GO:0001056 -name: RNA polymerase III activity +name: obsolete RNA polymerase III activity namespace: molecular_function -def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase III specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase III specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity. synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase III promoter" EXACT [] -xref: EC:2.7.7.6 {source="skos:broadMatch"} -intersection_of: GO:0003899 ! DNA-directed 5'-3' RNA polymerase activity -intersection_of: part_of GO:0006383 ! transcription by RNA polymerase III -relationship: occurs_in GO:0000785 ! chromatin -relationship: part_of GO:0006383 ! transcription by RNA polymerase III +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI +is_obsolete: true +replaced_by: GO:0003899 created_by: krc creation_date: 2010-09-23T03:44:47Z [Term] id: GO:0001057 -name: RNA polymerase IV activity +name: obsolete RNA polymerase IV activity namespace: molecular_function -def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase IV specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase IV specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity. synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase IV promoter" EXACT [] -xref: EC:2.7.7.6 {source="skos:broadMatch"} -intersection_of: GO:0003899 ! DNA-directed 5'-3' RNA polymerase activity -intersection_of: part_of GO:0001059 ! transcription by RNA polymerase IV -relationship: occurs_in GO:0000785 ! chromatin -relationship: part_of GO:0001059 ! transcription by RNA polymerase IV +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI +is_obsolete: true +replaced_by: GO:0003899 created_by: krc creation_date: 2010-09-23T03:44:55Z [Term] id: GO:0001058 -name: RNA polymerase V activity +name: obsolete RNA polymerase V activity namespace: molecular_function -def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase V specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase V specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity. synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase V promoter" EXACT [] -xref: EC:2.7.7.6 {source="skos:broadMatch"} -intersection_of: GO:0003899 ! DNA-directed 5'-3' RNA polymerase activity -intersection_of: part_of GO:0001060 ! transcription by RNA polymerase V -relationship: occurs_in GO:0000785 ! chromatin -relationship: part_of GO:0001060 ! transcription by RNA polymerase V +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI +is_obsolete: true +replaced_by: GO:0003899 created_by: krc creation_date: 2010-09-23T03:45:01Z @@ -7890,35 +7884,40 @@ creation_date: 2010-10-19T03:46:46Z [Term] id: GO:0001064 -name: single subunit type RNA polymerase activity +name: obsolete single subunit type RNA polymerase activity namespace: molecular_function -def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single-subunit-type RNA polymerase-specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single-subunit-type RNA polymerase-specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity. synonym: "T3/T7 type RNA polymerase activity" EXACT [] -is_a: GO:0003899 ! DNA-directed 5'-3' RNA polymerase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI +is_obsolete: true +replaced_by: GO:0003899 created_by: krc creation_date: 2010-10-19T03:47:56Z [Term] id: GO:0001065 -name: mitochondrial single subunit type RNA polymerase activity +name: obsolete mitochondrial single subunit type RNA polymerase activity namespace: molecular_function -def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single-subunit-type mitochondrial RNA polymerase-specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] -xref: EC:2.7.7.6 {source="skos:broadMatch"} -intersection_of: GO:0001064 ! single subunit type RNA polymerase activity -intersection_of: part_of GO:0006390 ! mitochondrial transcription +def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single-subunit-type mitochondrial RNA polymerase-specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] +comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity. +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI +is_obsolete: true +replaced_by: GO:0003899 created_by: krc creation_date: 2010-10-19T03:50:51Z [Term] id: GO:0001066 -name: plastid single subunit type RNA polymerase activity +name: obsolete plastid single subunit type RNA polymerase activity namespace: molecular_function -def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single subunit type plastid RNA polymerase specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH, PMID:20701995] -xref: EC:2.7.7.6 {source="skos:broadMatch"} -is_a: GO:0001064 ! single subunit type RNA polymerase activity -relationship: part_of GO:0042793 ! plastid transcription +def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single subunit type plastid RNA polymerase specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH, PMID:20701995] +comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity. +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI +is_obsolete: true +replaced_by: GO:0003899 created_by: krc creation_date: 2010-10-19T03:54:57Z @@ -32379,16 +32378,16 @@ is_obsolete: true [Term] id: GO:0003896 -name: DNA primase activity +name: obsolete DNA primase activity namespace: molecular_function alt_id: GO:0003897 alt_id: GO:0003898 -def: "Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases. In certain conditions, for example in response to DNA damage, some primases synthesize a DNA primer." [GOC:mah, GOC:mcc, PMID:11395402, PMID:26184436, PMID:38203225, PMID:38492718] -xref: EC:2.7.7.101 {source="skos:narrowMatch"} -xref: EC:2.7.7.102 {source="skos:narrowMatch"} -is_a: GO:0003899 ! DNA-directed 5'-3' RNA polymerase activity -relationship: part_of GO:0006269 ! DNA replication, synthesis of primer +def: "OBSOLETE. Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases. In certain conditions, for example in response to DNA damage, some primases synthesize a DNA primer." [GOC:mah, GOC:mcc, PMID:11395402, PMID:26184436, PMID:38203225, PMID:38492718] +comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity. +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27176" xsd:anyURI +is_obsolete: true +replaced_by: GO:0003899 [Term] id: GO:0003899 @@ -54021,7 +54020,6 @@ synonym: "pol-prim" RELATED [] synonym: "primosome" BROAD [] is_a: GO:0055029 ! nuclear DNA-directed RNA polymerase complex relationship: capable_of GO:0003887 ! DNA-directed DNA polymerase activity -relationship: capable_of GO:0003896 ! DNA primase activity relationship: part_of GO:0000228 ! nuclear chromosome relationship: part_of GO:0043601 ! nuclear replisome @@ -54091,10 +54089,9 @@ namespace: cellular_component def: "RNA polymerase III, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces 5S rRNA, tRNAs and some of the small nuclear RNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase I and others of which are also found in RNA polymerases I and II. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template." [GOC:krc, GOC:mtg_sensu] synonym: "DNA-directed RNA polymerase III activity" RELATED [] synonym: "DNA-directed RNA polymerase III complex" EXACT [] +is_a: GO:0000428 ! DNA-directed RNA polymerase complex is_a: GO:0140513 ! nuclear protein-containing complex -intersection_of: GO:0000428 ! DNA-directed RNA polymerase complex -intersection_of: capable_of GO:0001056 ! RNA polymerase III activity -intersection_of: part_of GO:0005634 ! nucleus +relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005667 @@ -531378,10 +531375,10 @@ creation_date: 2014-11-19T18:24:29Z [Term] id: GO:1903623 -name: negative regulation of RNA polymerase III activity +name: obsolete negative regulation of RNA polymerase III activity namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA polymerase III activity." [GO_REF:0000059, GOC:TermGenie, PMID:25392932] -subset: gocheck_obsoletion_candidate +def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of RNA polymerase III activity." [GO_REF:0000059, GOC:TermGenie, PMID:25392932] +comment: This term was obsoleted because it represents a molecular function. synonym: "down regulation of DNA-directed RNA polymerase activity involved in transcription from RNA polymerase III promoter" EXACT [GOC:TermGenie] synonym: "down regulation of RNA polymerase III activity" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA-directed RNA polymerase activity involved in transcription from RNA polymerase III promoter" EXACT [GOC:TermGenie] @@ -531391,9 +531388,8 @@ synonym: "downregulation of RNA polymerase III activity" EXACT [GOC:TermGenie] synonym: "inhibition of DNA-directed RNA polymerase activity involved in transcription from RNA polymerase III promoter" NARROW [GOC:TermGenie] synonym: "inhibition of RNA polymerase III activity" NARROW [GOC:TermGenie] synonym: "negative regulation of DNA-directed RNA polymerase activity involved in transcription from RNA polymerase III promoter" EXACT [GOC:TermGenie] -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0001056 ! RNA polymerase III activity -relationship: negatively_regulates GO:0006383 {http://purl.obolibrary.org/obo/IAO_0000233="https://github.com/geneontology/go-ontology/issues/13926"} ! transcription by RNA polymerase III +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI +is_obsolete: true created_by: al creation_date: 2014-11-19T18:24:37Z @@ -537229,18 +537225,16 @@ creation_date: 2015-02-12T14:28:36Z [Term] id: GO:1903934 -name: positive regulation of DNA primase activity +name: obsolete positive regulation of DNA primase activity namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of DNA primase activity." [GO_REF:0000059, GOC:TermGenie, PMID:14766746] -subset: gocheck_obsoletion_candidate +def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of DNA primase activity." [GO_REF:0000059, GOC:TermGenie, PMID:14766746] +comment: This term was obsoleted because it represents a molecular function. synonym: "activation of DNA primase activity" NARROW [GOC:TermGenie] synonym: "up regulation of DNA primase activity" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA primase activity" EXACT [GOC:TermGenie] synonym: "upregulation of DNA primase activity" EXACT [GOC:TermGenie] -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0003896 ! DNA primase activity -relationship: positively_regulates GO:0006259 {http://purl.obolibrary.org/obo/IAO_0000233="https://github.com/geneontology/go-ontology/issues/13926"} ! DNA metabolic process -relationship: positively_regulates GO:0032774 {http://purl.obolibrary.org/obo/IAO_0000233="https://github.com/geneontology/go-ontology/issues/13926"} ! RNA biosynthetic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI +is_obsolete: true created_by: mah creation_date: 2015-02-12T14:28:45Z