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geneontology / amigo

AmiGO is the public interface for the Gene Ontology.
http://amigo.geneontology.org
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Incorrect parentage shown in AmiGO #558

Open pgaudet opened 5 years ago

pgaudet commented 5 years ago

Hello, GO:0034061 DNA polymerase activity and GO:0003964 RNA-directed DNA polymerase activity look like direct children of 'catalytic activity' in AmiGO, but they are not. Why the discrepancy ?

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Thanks, Pascale

ValWood commented 5 years ago

We have a bug, only spotted today, it might be related? https://www.pombase.org/browse-curation/fission-yeast-go-slim-terms

Kim hasn't changed our code locally and we are sure that it was working previously. I wondered if it is anything to do with relationship changes...

ukemi commented 5 years ago

When I look at the editors' version of the ontology in Protege, I see that DNA polymerase activity is asserted to be a catalytic activity, acting on DNA and RNA-directed DNA polymerase activity is an asserted child of DNA polymerase activity.

This is also reflected in the snapshot files: go-basic.obo [Term] id: GO:0003964 name: RNA-directed DNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time." [EC:2.7.7.49] synonym: "deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity" EXACT [EC:2.7.7.49] synonym: "DNA nucleotidyltransferase (RNA-directed) activity" EXACT [EC:2.7.7.49] synonym: "reverse transcriptase activity" EXACT [EC:2.7.7.49] synonym: "revertase activity" RELATED [EC:2.7.7.49] synonym: "RNA revertase activity" EXACT [EC:2.7.7.49] synonym: "RNA-dependent deoxyribonucleate nucleotidyltransferase activity" EXACT [EC:2.7.7.49] synonym: "RNA-dependent DNA polymerase activity" EXACT [EC:2.7.7.49] synonym: "RNA-directed DNA polymerase, group II intron encoded" NARROW [] synonym: "RNA-directed DNA polymerase, transposon encoded" NARROW [] synonym: "RNA-instructed DNA polymerase activity" EXACT [EC:2.7.7.49] synonym: "RT" RELATED [EC:2.7.7.49] xref: EC:2.7.7.49 xref: MetaCyc:RNA-DIRECTED-DNA-POLYMERASE-RXN xref: reactome:R-HSA-164504 "Synthesis of minus strand strong stop DNA (-sssDNA)" xref: reactome:R-HSA-164520 "Minus strand DNA synthesis resumes" is_a: GO:0034061 ! DNA polymerase activity

[Term] id: GO:0034061 name: DNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group." [EC:2.7.7.7, GOC:mah] synonym: "deoxynucleate polymerase activity" EXACT [EC:2.7.7.7] synonym: "deoxyribonucleate nucleotidyltransferase activity" EXACT [EC:2.7.7.7] synonym: "deoxyribonucleic acid polymerase activity" EXACT [EC:2.7.7.7] synonym: "deoxyribonucleic polymerase activity" EXACT [EC:2.7.7.7] synonym: "DNA nucleotidyltransferase activity" EXACT [EC:2.7.7.7] is_a: GO:0016779 ! nucleotidyltransferase activity is_a: GO:0140097 ! catalytic activity, acting on DNA

This is in today's snapshot of go.obo [Term] id: GO:0003964 name: RNA-directed DNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time." [EC:2.7.7.49] synonym: "deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity" EXACT [EC:2.7.7.49] synonym: "DNA nucleotidyltransferase (RNA-directed) activity" EXACT [EC:2.7.7.49] synonym: "reverse transcriptase activity" EXACT [EC:2.7.7.49] synonym: "revertase activity" RELATED [EC:2.7.7.49] synonym: "RNA revertase activity" EXACT [EC:2.7.7.49] synonym: "RNA-dependent deoxyribonucleate nucleotidyltransferase activity" EXACT [EC:2.7.7.49] synonym: "RNA-dependent DNA polymerase activity" EXACT [EC:2.7.7.49] synonym: "RNA-directed DNA polymerase, group II intron encoded" NARROW [] synonym: "RNA-directed DNA polymerase, transposon encoded" NARROW [] synonym: "RNA-instructed DNA polymerase activity" EXACT [EC:2.7.7.49] synonym: "RT" RELATED [EC:2.7.7.49] xref: EC:2.7.7.49 xref: MetaCyc:RNA-DIRECTED-DNA-POLYMERASE-RXN xref: reactome:R-HSA-164504 "Synthesis of minus strand strong stop DNA (-sssDNA)" xref: reactome:R-HSA-164520 "Minus strand DNA synthesis resumes" is_a: GO:0034061 ! DNA polymerase activity relationship: part_of GO:0006278 ! RNA-dependent DNA biosynthetic process

[Term] id: GO:0034061 name: DNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group." [EC:2.7.7.7, GOC:mah] synonym: "deoxynucleate polymerase activity" EXACT [EC:2.7.7.7] synonym: "deoxyribonucleate nucleotidyltransferase activity" EXACT [EC:2.7.7.7] synonym: "deoxyribonucleic acid polymerase activity" EXACT [EC:2.7.7.7] synonym: "deoxyribonucleic polymerase activity" EXACT [EC:2.7.7.7] synonym: "DNA nucleotidyltransferase activity" EXACT [EC:2.7.7.7] is_a: GO:0016779 ! nucleotidyltransferase activity is_a: GO:0140097 ! catalytic activity, acting on DNA relationship: part_of GO:0071897 ! DNA biosynthetic process

So at the source file level, this all looks ok to me.

ValWood commented 5 years ago

OK our problem was a different problem...

kltm commented 5 years ago

Other possible expressions: https://github.com/geneontology/amigo/issues/525

pgaudet commented 5 years ago

Is #525 the same thing ? In #525 you talk about recent changes in the ontology. I dont think the two terms here were edited recently.