Gene Ontology Classification GAF format
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7.8 years ago

Where can I get, an easy to parse file, with all the gene ontology IDs and their respective classification (biological processes, cellular components and molecular functions)? Something like csv or tsv format in two columns.

I want this in order to generate a GAF file format, I already have the gene ontology IDs for my list of "interesting genes".

The final file should be like this, where P = biological process, F = molecular function or C = cellular component.

UniProtKB A0A060WYW4 GSONMT00014026001 GO:0016042 PMID:22626869 IMP P Uncharacterized protein A0A060WYW4_ONCMY|GSONMT00014026001 protein taxon:8022 20151016 AgBase occurs_in(CL:0000136)
UniProtKB A0A060WZC7 GSONMT00004066001 GO:0014802 PMID:9857007 IDA C Uncharacterized protein A0A060WZC7_ONCMY|GSONMT00004066001 protein taxon:8022 20150706 AgBase part_of(UBERON:0001134) UniProtKB A0A060WZC7 GSONMT00004066001 GO:0014808 PMID:9857007 IMP P Uncharacterized protein A0A060WZC7_ONCMY|GSONMT00004066001 protein taxon:8022 20150706 AgBase occurs_in(UBERON:0001134),occurs_in(GO:0014802) UniProtKB A0A060WZC7 GSONMT00004066001 GO:0015643 PMID:9857007 IDA F Uncharacterized protein A0A060WZC7_ONCMY|GSONMT00004066001 protein taxon:8022 20150707 AgBase occurs_in(UBERON:0001134),has_direct_input(CHEBI:8925)
UniProtKB A0A060WZC7 GSONMT00004066001 GO:0016020 PMID:9857007 IDA C Uncharacterized protein A0A060WZC7_ONCMY|GSONMT00004066001 protein taxon:8022 20150706 AgBase part_of(UBERON:0001134) UniProtKB A0A060WZN4 GSONMT00045295001 GO:0005497 PMID:18339711 IDA F Uncharacterized protein A0A060WZN4_ONCMY|GSONMT00045295001 protein taxon:8022 20160224 AgBase
UniProtKB A0A060WZN4 GSONMT00045295001 GO:0005615 PMID:18339711 IDA C Uncharacterized protein A0A060WZN4_ONCMY|GSONMT00045295001 protein taxon:8022 20160224 AgBase
UniProtKB A0A060WZN4 GSONMT00045295001 GO:0005623 PMID:18339711 IDA C Uncharacterized protein A0A060WZN4_ONCMY|GSONMT00045295001 protein taxon:8022 20160224 AgBase part_of(CL:0000501)|part_of(CL:0000503) UniProtKB A0A060WZN4 GSONMT00045295001 GO:1903924 PMID:18339711 IDA F Uncharacterized protein A0A060WZN4_ONCMY|GSONMT00045295001 protein taxon:8022 20160224 AgBase
UniProtKB A0A060WZN4 GSONMT00045295001 GO:1990239 PMID:18339711 IDA F Uncharacterized protein A0A060WZN4_ONCMY|GSONMT00045295001 protein taxon:8022 20160224 AgBase

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it is may be a duplicate of Retrieve GO terms ontology

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Entering edit mode
7.8 years ago

The Gene Ontology OBO file has the domain each term belongs to in the "name_space" field. Alternatively, you can get it from the MySQL database. The query is:

select term_type from term where acc='GO:2001317';
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