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:0046872 GO_REF:0000043 IEA #> 3 UniProtKB A0A024RBG1 NUDT4B enables GO:0052840 GO_REF:0000003 IEA #> 4 UniProtKB A0A024RBG1 NUDT4B enables GO:0052842 GO_REF:0000003 IEA #> 5 UniProtKB A0A024RBG1 NUDT4B located_in GO:0005829 GO_REF:0000052 IDA #> 6 UniProtKB A0A075B6H7 IGKV3-7 involved_in GO:0002250 GO_REF:0000043 IEA #> with_from ontology #> 1 UniProtKB-KW:KW-0694 F #> 2 UniProtKB-KW:KW-0479 F #> 3 EC:3.6.1.52 F #> 4 EC:3.6.1.52 F #> 5 C #> 6 UniProtKB-KW:KW-1064 P #> 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 Probable non-functional immunoglobulin kappa variable 3-7 IGKV3-7 protein #> taxon date assigned_by annotation_extension gene_product_form_id #> 1 taxon:9606 20210612 UniProt NA #> 2 taxon:9606 20210612 UniProt NA #> 3 taxon:9606 20210612 UniProt NA #> 4 taxon:9606 20210612 UniProt NA #> 5 taxon:9606 20161204 HPA NA #> 6 taxon:9606 20210612 UniProt NA
# }