Fetch gene ontology information from geneontology.org

Source: R/fetch_go.R

Fetches gene ontology data from geneontology.org for the provided organism ID.

fetch_go(organism_id)

Arguments

organism_id

a character value NCBI taxonomy identifier of an organism (TaxId). Possible inputs inlude only: "9606" (Human), "559292" (Yeast) and "83333" (E. coli).

Value

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/

Examples

# \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:0005515  PMID:33961781      IPI
#> 3 UniProtKB A0A024RBG1 NUDT4B   enables GO:0008486 GO_REF:0000003      IEA
#> 4 UniProtKB A0A024RBG1 NUDT4B   enables GO:0016462 GO_REF:0000002      IEA
#> 5 UniProtKB A0A024RBG1 NUDT4B   enables GO:0016787 GO_REF:0000002      IEA
#> 6 UniProtKB A0A024RBG1 NUDT4B   enables GO:0016787 GO_REF:0000043      IEA
#>              with_from ontology
#> 1 UniProtKB-KW:KW-0694        F
#> 2     UniProtKB:Q8NFP7        F
#> 3          EC:3.6.1.52        F
#> 4   InterPro:IPR047198        F
#> 5   InterPro:IPR020084        F
#> 6 UniProtKB-KW:KW-0378        F
#>                                                      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 Diphosphoinositol polyphosphate phosphohydrolase NUDT4B   NUDT4B protein
#> 5 Diphosphoinositol polyphosphate phosphohydrolase NUDT4B   NUDT4B protein
#> 6 Diphosphoinositol polyphosphate phosphohydrolase NUDT4B   NUDT4B protein
#>        taxon     date assigned_by annotation_extension gene_product_form_id
#> 1 taxon:9606 20251006     UniProt                      UniProtKB:A0A024RBG1
#> 2 taxon:9606 20251004      IntAct                      UniProtKB:A0A024RBG1
#> 3 taxon:9606 20251006     UniProt                      UniProtKB:A0A024RBG1
#> 4 taxon:9606 20251006    InterPro                      UniProtKB:A0A024RBG1
#> 5 taxon:9606 20251006    InterPro                      UniProtKB:A0A024RBG1
#> 6 taxon:9606 20251006     UniProt                      UniProtKB:A0A024RBG1
# }