Gene Ontology is an ontology of gene subcellular localizations, molecular functions and involvement in biological processes. Gene products across many organisms are annotated with the ontology terms. This function downloads the gene-ontology term associations for certain model organisms or all organisms. For a description of the columns see http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/.
Usage
go_annot_download(organism = "human", aspects = c("C", "F", "P"), slim = NULL)Arguments
- organism
Character: either "chicken", "cow", "dog", "human", "pig" or "uniprot_all".
- aspects
Character vector with some of the following elements: "C" (cellular component), "F" (molecular function) and "P" (biological process). Gene Ontology is three separate ontologies called as three aspects. By this parameter you can control which aspects to include in the output.
- slim
Character: if not
NULL, the name of a GOsubset (slim). instead of the full GO annotation, the slim annotation will be returned. See details atgo_annot_slim. IfTRUE, the "generic" slim will be used.
Examples
goa_data <- go_annot_download()
goa_data
#> # A tibble: 638,732 × 17
#> db db_object_id db_object_symbol qualifier go_id db_ref evidence_code
#> <fct> <chr> <chr> <fct> <chr> <chr> <fct>
#> 1 UniProtKB A0A024RBG1 NUDT4B enables GO:0… GO_RE… IEA
#> 2 UniProtKB A0A024RBG1 NUDT4B enables GO:0… GO_RE… IEA
#> 3 UniProtKB A0A024RBG1 NUDT4B located_in GO:0… GO_RE… IDA
#> 4 UniProtKB A0A075B6H7 IGKV3-7 involved_… GO:0… GO_RE… IEA
#> 5 UniProtKB A0A075B6H7 IGKV3-7 located_in GO:0… GO_RE… IEA
#> 6 UniProtKB A0A075B6H7 IGKV3-7 part_of GO:0… GO_RE… IEA
#> 7 UniProtKB A0A075B6H8 IGKV1D-42 involved_… GO:0… GO_RE… IEA
#> 8 UniProtKB A0A075B6H8 IGKV1D-42 located_in GO:0… GO_RE… IEA
#> 9 UniProtKB A0A075B6H8 IGKV1D-42 part_of GO:0… GO_RE… IEA
#> 10 UniProtKB A0A075B6H9 IGLV4-69 involved_… GO:0… GO_RE… IEA
#> # ℹ 638,722 more rows
#> # ℹ 10 more variables: with_or_from <chr>, aspect <fct>, db_object_name <chr>,
#> # db_object_synonym <chr>, db_object_type <fct>, taxon <fct>, date <date>,
#> # assigned_by <fct>, annotation_extension <chr>, gene_product_from_id <chr>
# # A tibble: 606,840 x 17
# db db_object_id db_object_symbol qualifier go_id db_ref
# <fct> <chr> <chr> <fct> <chr> <chr>
# 1 UniProt. A0A024RBG1 NUDT4B NA GO:000. GO_REF:00.
# 2 UniProt. A0A024RBG1 NUDT4B NA GO:000. GO_REF:00.
# 3 UniProt. A0A024RBG1 NUDT4B NA GO:004. GO_REF:00.
# 4 UniProt. A0A024RBG1 NUDT4B NA GO:005. GO_REF:00.
# 5 UniProt. A0A024RBG1 NUDT4B NA GO:005. GO_REF:00.
# # . with 606,830 more rows, and 11 more variables:
# # evidence_code <fct>, with_or_from <chr>, aspect <fct>,
# # db_object_name <chr>, db_object_synonym <chr>,
# # db_object_type <fct>, taxon <fct>, date <date>,
# # assigned_by <fct>, annotation_extension <chr>,
# # gene_product_from_id <chr>