Fetches gene ontology data from geneontology.org for the provided organism ID.
fetch_go(organism_id)a character value NCBI taxonomy identifier of an organism (TaxId). Possible inputs inlude only: "9606" (Human), "559292" (Yeast) and "83333" (E. coli).
A data frame that contains gene ontology mappings to UniProt or SGD IDs. The original file is a .GAF file. A detailed description of all columns can be found here: http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/
# \donttest{
go <- fetch_go("9606")
head(go)
#> db db_id symbol qualifier go_id db_reference evidence
#> 1 UniProtKB A0A024RBG1 NUDT4B enables GO:0003723 GO_REF:0000043 IEA
#> 2 UniProtKB A0A024RBG1 NUDT4B enables GO:0046872 GO_REF:0000043 IEA
#> 3 UniProtKB A0A024RBG1 NUDT4B located_in GO:0005829 GO_REF:0000052 IDA
#> 4 UniProtKB A0A075B6H7 IGKV3-7 involved_in GO:0002250 GO_REF:0000043 IEA
#> 5 UniProtKB A0A075B6H7 IGKV3-7 located_in GO:0005886 GO_REF:0000044 IEA
#> 6 UniProtKB A0A075B6H7 IGKV3-7 part_of GO:0019814 GO_REF:0000043 IEA
#> with_from ontology
#> 1 UniProtKB-KW:KW-0694 F
#> 2 UniProtKB-KW:KW-0479 F
#> 3 C
#> 4 UniProtKB-KW:KW-1064 P
#> 5 UniProtKB-SubCell:SL-0039 C
#> 6 UniProtKB-KW:KW-1280 C
#> name synonyme type
#> 1 Diphosphoinositol polyphosphate phosphohydrolase NUDT4B NUDT4B protein
#> 2 Diphosphoinositol polyphosphate phosphohydrolase NUDT4B NUDT4B protein
#> 3 Diphosphoinositol polyphosphate phosphohydrolase NUDT4B NUDT4B protein
#> 4 Probable non-functional immunoglobulin kappa variable 3-7 IGKV3-7 protein
#> 5 Probable non-functional immunoglobulin kappa variable 3-7 IGKV3-7 protein
#> 6 Probable non-functional immunoglobulin kappa variable 3-7 IGKV3-7 protein
#> taxon date assigned_by annotation_extension gene_product_form_id
#> 1 taxon:9606 20231122 UniProt NA
#> 2 taxon:9606 20231122 UniProt NA
#> 3 taxon:9606 20230619 HPA NA
#> 4 taxon:9606 20231122 UniProt NA
#> 5 taxon:9606 20231122 UniProt NA
#> 6 taxon:9606 20231122 UniProt NA
# }