Skip to contents

Get a Proteome by UPID

Source: R/uniprot_proteomes.R
rba_uniprot_proteomes.Rd

UniProt collects and annotates proteomes (protein sets expressed in an organism). Retrieve a proteome's metadata by UPID, optionally including its proteins. When proteins are requested, they can be filtered by UniProtKB review status. See What are proteomes? for more information.

Usage

rba_uniprot_proteomes(upid, get_proteins = FALSE, reviewed = NULL, ...)

Arguments

upid

Character: UniProt Proteome identifier (UPID).

get_proteins

Logical: (default = FALSE) If TRUE, embed the proteins belonging to the supplied proteome in its genome components.

reviewed

Logical: (optional) Used only when get_proteins is TRUE. If TRUE, return only reviewed UniProtKB/Swiss-Prot proteins; if FALSE, return only unreviewed UniProtKB/TrEMBL entries; if NULL, do not filter by review status.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A list containing the requested proteome. With get_proteins = TRUE, protein entries are included under each element of component.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/proteomes/proteins/{upid}"
"GET https://www.ebi.ac.uk/proteins/api/proteomes/{upid}"

References

  • The UniProt Consortium. (2025). UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research, 53(D1), D609–D617. https://doi.org/10.1093/nar/gkae1010

  • Nightingale, A., Antunes, R., Alpi, E., Bursteinas, B., Gonzales, L., Liu, W., Luo, J., Qi, G., Turner, E., & Martin, M. (2017). The Proteins API: Accessing key integrated protein and genome information. Nucleic Acids Research, 45(W1), W539–W544. https://doi.org/10.1093/nar/gkx237

  • Proteins API Documentation

  • Citations note on UniProt website

See also

Other "UniProt - Proteomes": rba_uniprot_genecentric(), rba_uniprot_genecentric_search(), rba_uniprot_proteomes_search()

Examples

# \donttest{
rba_uniprot_proteomes(upid = "UP000000354")
# }
# \donttest{
rba_uniprot_proteomes(upid = "UP000000354", get_proteins = TRUE)
# }