From 7c7ba9a91fcabd911a2d1c7aa66fbb8d92e51f8e Mon Sep 17 00:00:00 2001 From: Raymond Lee Date: Tue, 20 Aug 2024 17:34:15 -0700 Subject: [PATCH] Obsoleted GO:0106339; #28550. --- src/ontology/go-edit.obo | 34 ++++---- .../go-catalytic-activities-participants.owl | 47 +---------- src/ontology/imports/go_taxon_constraints.owl | 79 +++++-------------- src/taxon_constraints/never_in_taxon.ofn | 12 +-- src/taxon_constraints/never_in_taxon.tsv | 2 +- src/taxon_constraints/only_in_taxon.ofn | 6 ++ 6 files changed, 51 insertions(+), 129 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 962f8db5d7..3d9c33954a 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -337183,7 +337183,7 @@ synonym: "tRNA cytosine-2'-O-methyltransferase activity" EXACT [] property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26018" xsd:anyURI is_obsolete: true consider: GO:0106059 -consider: GO:0106339 +consider: GO:0106340 created_by: ai creation_date: 2010-10-11T01:05:47Z @@ -441958,37 +441958,37 @@ creation_date: 2020-11-05T17:56:43Z [Term] id: GO:0106339 -name: tRNA (cytidine(32)-2'-O)-methyltransferase activity +name: obsolete tRNA (cytidine(32)-2'-O)-methyltransferase activity namespace: molecular_function -def: "Catalysis of the reaction: cytidine(32) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(32) in tRNA + H+ + S-adenosyl-L-homocysteine." [PMID:25404562, RHEA:42932] +def: "OBSOLETE. Catalysis of the reaction: cytidine(32) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(32) in tRNA + H+ + S-adenosyl-L-homocysteine." [PMID:25404562] +comment: The reason for obsoletion is that this term is equivalent to tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase activity. synonym: "tRNA (cytidine 32-2'-O)-methyltransferase activity" EXACT [] -xref: EC:2.1.1.200 {source="skos:broadMatch"} -xref: EC:2.1.1.205 {source="skos:broadMatch"} -xref: MetaCyc:RXN-11866 {source="skos:exactMatch"} -xref: RHEA:42396 {source="skos:broadMatch"} -xref: RHEA:42932 {source="skos:exactMatch"} -is_a: GO:0016427 ! tRNA (cytidine) methyltransferase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24771" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26018" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26086" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28550" xsd:anyURI +is_obsolete: true +replaced_by: GO:0106340 created_by: hjd creation_date: 2020-11-05T22:48:53Z [Term] id: GO:0106340 -name: tRNA (guanine(34)-2'-O)-methyltransferase activity -namespace: molecular_function -def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine 34 in tRNA= S-adenosyl-L-homocysteine + 2'-O-methylguanosine 34 in tRNA." [PMID:25404562] -synonym: "tRNA (guanosine 34-2'-O)-methyltransferase activity" EXACT [] -synonym: "tRNA (guanosine(34)-2'-O)-methyltransferase activity" EXACT [] -xref: EC:2.1.1.205 {source="skos:broadMatch"} -xref: MetaCyc:RXN-11868 {source="skos:exactMatch"} -xref: RHEA:42396 {source="skos:broadMatch"} +name: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase activity +namespace: molecular_function +def: "Catalysis of the reaction: cytidine(32)/guanosine(34) in tRNA + 2 S-adenosyl-L-methionine = 2'-O-methylcytidine(32)/2'-O-methylguanosine(34) in tRNA + 2 H+ + 2 S-adenosyl-L-homocysteine." [RHEA:42396] +synonym: "tRNA (cytidine 32-2'-O)-methyltransferase activity" NARROW [] +synonym: "tRNA (cytidine(32)-2'-O)-methyltransferase activity" NARROW [] +synonym: "tRNA (guanosine 34-2'-O)-methyltransferase activity" NARROW [] +synonym: "tRNA (guanosine(34)-2'-O)-methyltransferase activity" NARROW [] +xref: EC:2.1.1.205 +xref: RHEA:42396 is_a: GO:0016423 ! tRNA (guanine) methyltransferase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25257" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26085" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26086" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28550" xsd:anyURI created_by: hjd creation_date: 2020-11-05T22:52:49Z diff --git a/src/ontology/imports/go-catalytic-activities-participants.owl b/src/ontology/imports/go-catalytic-activities-participants.owl index 76d050a56c..71b9f24639 100644 --- a/src/ontology/imports/go-catalytic-activities-participants.owl +++ b/src/ontology/imports/go-catalytic-activities-participants.owl @@ -175056,50 +175056,7 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -184748,5 +184705,5 @@ - + diff --git a/src/ontology/imports/go_taxon_constraints.owl b/src/ontology/imports/go_taxon_constraints.owl index 114ec85d3d..62e8442a1a 100644 --- a/src/ontology/imports/go_taxon_constraints.owl +++ b/src/ontology/imports/go_taxon_constraints.owl @@ -33397,49 +33397,8 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID:18068186 - - - - - - PMID:18068186 - - - - - - PMID:18068186 - @@ -34684,27 +34643,27 @@ - - + + - + - + - + PMID:24739148 - + PMID:24739148 @@ -34732,27 +34691,27 @@ - - + + - + - + - + PMID:15557260 - + PMID:15557260 @@ -34761,27 +34720,27 @@ - - + + - + - + - + PMID:31546611 - + PMID:31546611 @@ -37766,5 +37725,5 @@ - + diff --git a/src/taxon_constraints/never_in_taxon.ofn b/src/taxon_constraints/never_in_taxon.ofn index f3a7d859ac..9812fc689b 100644 --- a/src/taxon_constraints/never_in_taxon.ofn +++ b/src/taxon_constraints/never_in_taxon.ofn @@ -372,7 +372,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3751,12 +3751,12 @@ DisjointClasses( ObjectSomeValuesFrom DisjointClasses( ObjectSomeValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: () +# Class: () -AnnotationAssertion(Annotation( "PMID:18068186"^^xsd:string) ) -SubClassOf(Annotation( "PMID:18068186"^^xsd:string) ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "PMID:18068186"^^xsd:string) ObjectSomeValuesFrom( ObjectComplementOf())) -DisjointClasses(Annotation( "PMID:18068186"^^xsd:string) ObjectSomeValuesFrom( )) +AnnotationAssertion(Annotation( "PMID:18068186"^^xsd:string) ) +SubClassOf(Annotation( "PMID:18068186"^^xsd:string) ObjectComplementOf(ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "PMID:18068186"^^xsd:string) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(Annotation( "PMID:18068186"^^xsd:string) ObjectSomeValuesFrom( )) # Class: () diff --git a/src/taxon_constraints/never_in_taxon.tsv b/src/taxon_constraints/never_in_taxon.tsv index 7c663837a3..49a43aec25 100644 --- a/src/taxon_constraints/never_in_taxon.tsv +++ b/src/taxon_constraints/never_in_taxon.tsv @@ -574,7 +574,7 @@ GO:0003365 establishment of cell polarity involved in ameboidal cell migration N GO:0090398 cellular senescence NCBITaxon:4751 Fungi GO:0000365 mRNA trans splicing, via spliceosome NCBITaxon:4751 Fungi GO:0016477 cell migration NCBITaxon:4890 Ascomycota -GO:0106339 tRNA (cytidine 32-2'-O)-methyltransferase activity NCBITaxon:2157 Archaea PMID:18068186 +GO:0106340 tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase activity NCBITaxon:2157 Archaea PMID:18068186 GO:0035658 Piccolo NuA4 histone acetyltransferase complex NCBITaxon:4896 Schizosaccharomyces pombe PMID:37550452 GO:0002224 toll-like receptor signaling pathway NCBITaxon:7215 Drosophila PMID:30034391 GO:0017015 regulation of transforming growth factor beta receptor signaling pathway NCBITaxon:4751 Fungi diff --git a/src/taxon_constraints/only_in_taxon.ofn b/src/taxon_constraints/only_in_taxon.ofn index a1f6e572eb..8cc634be63 100644 --- a/src/taxon_constraints/only_in_taxon.ofn +++ b/src/taxon_constraints/only_in_taxon.ofn @@ -178,6 +178,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1838,6 +1839,11 @@ SubClassOf( ObjectAllValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) +# Class: () + +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + # Class: () SubClassOf( ObjectSomeValuesFrom( ))