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: 630,196 × 17
#> db db_ob…¹ db_ob…² quali…³ go_id db_ref evide…⁴ with_…⁵ aspect db_ob…⁶
#> <fct> <chr> <chr> <fct> <chr> <chr> <fct> <chr> <fct> <chr>
#> 1 UniProtKB A0A024… NUDT4B enables GO:0… GO_RE… IEA UniPro… F Diphos…
#> 2 UniProtKB A0A024… NUDT4B enables GO:0… GO_RE… IEA UniPro… F Diphos…
#> 3 UniProtKB A0A024… NUDT4B locate… GO:0… GO_RE… IDA NA C Diphos…
#> 4 UniProtKB A0A075… IGKV3-7 involv… GO:0… GO_RE… IEA UniPro… P Probab…
#> 5 UniProtKB A0A075… IGKV3-7 locate… GO:0… GO_RE… IEA UniPro… C Probab…
#> 6 UniProtKB A0A075… IGKV3-7 part_of GO:0… GO_RE… IEA UniPro… C Probab…
#> 7 UniProtKB A0A075… IGKV1D… involv… GO:0… GO_RE… IEA UniPro… P Probab…
#> 8 UniProtKB A0A075… IGKV1D… locate… GO:0… GO_RE… IEA UniPro… C Probab…
#> 9 UniProtKB A0A075… IGKV1D… part_of GO:0… GO_RE… IEA UniPro… C Probab…
#> 10 UniProtKB A0A075… IGLV4-… involv… GO:0… GO_RE… IEA UniPro… P Immuno…
#> # … with 630,186 more rows, 7 more variables: db_object_synonym <chr>,
#> # db_object_type <fct>, taxon <fct>, date <date>, assigned_by <fct>,
#> # annotation_extension <chr>, gene_product_from_id <chr>, and abbreviated
#> # variable names ¹db_object_id, ²db_object_symbol, ³qualifier,
#> # ⁴evidence_code, ⁵with_or_from, ⁶db_object_name
# # 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>