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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 at go_annot_slim. If TRUE, the "generic" slim will be used.

Value

A tibble (data frame) of annotations as it is provided by the database

Examples

goa_data <- go_annot_download()
goa_data
#> # A tibble: 616,308 × 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           enables    GO:0… GO_RE… IEA          
#>  4 UniProtKB A0A024RBG1   NUDT4B           enables    GO:0… GO_RE… IEA          
#>  5 UniProtKB A0A024RBG1   NUDT4B           located_in GO:0… GO_RE… IDA          
#>  6 UniProtKB A0A075B6H7   IGKV3-7          involved_… GO:0… GO_RE… IEA          
#>  7 UniProtKB A0A075B6H7   IGKV3-7          located_in GO:0… GO_RE… IEA          
#>  8 UniProtKB A0A075B6H7   IGKV3-7          part_of    GO:0… GO_RE… IEA          
#>  9 UniProtKB A0A075B6H8   IGKV1D-42        involved_… GO:0… GO_RE… IEA          
#> 10 UniProtKB A0A075B6H8   IGKV1D-42        located_in GO:0… GO_RE… IEA          
#> # … with 616,298 more rows, and 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>