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:0046872 GO_REF:0000043      IEA
#> 4 UniProtKB A0A024RBG1  NUDT4B  located_in GO:0005829 GO_REF:0000052      IDA
#> 5 UniProtKB A0A075B6H7 IGKV3-7 involved_in GO:0002250 GO_REF:0000043      IEA
#> 6 UniProtKB A0A075B6H7 IGKV3-7  located_in GO:0005886 GO_REF:0000044      IEA
#>                   with_from ontology
#> 1      UniProtKB-KW:KW-0694        F
#> 2          UniProtKB:Q8NFP7        F
#> 3      UniProtKB-KW:KW-0479        F
#> 4                                  C
#> 5      UniProtKB-KW:KW-1064        P
#> 6 UniProtKB-SubCell:SL-0039        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   Diphosphoinositol polyphosphate phosphohydrolase NUDT4B   NUDT4B 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 20240729     UniProt                      UniProtKB:A0A024RBG1
#> 2 taxon:9606 20240727      IntAct                      UniProtKB:A0A024RBG1
#> 3 taxon:9606 20240729     UniProt                      UniProtKB:A0A024RBG1
#> 4 taxon:9606 20230619         HPA                      UniProtKB:A0A024RBG1
#> 5 taxon:9606 20240729     UniProt                      UniProtKB:A0A075B6H7
#> 6 taxon:9606 20240729     UniProt                      UniProtKB:A0A075B6H7
# }