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Search Proteomes in UniProt

Source: R/uniprot_proteomes.R
rba_uniprot_proteomes_search.Rd

UniProt collects and annotates proteomes (protein sets expressed in an organism). Search available proteomes by name, identifier, taxonomy, keyword, cross-reference, genome accession, or status. See What are proteomes? for more information.

Usage

rba_uniprot_proteomes_search(
  name = NULL,
  upid = NULL,
  taxid = NULL,
  keyword = NULL,
  xref = NULL,
  genome_acc = NULL,
  is_ref_proteome = NULL,
  is_redundant = NULL,
  ...
)

Arguments

name

Character: (optional) A term in the proteome name.

upid

Character: (optional) UniProt Proteome identifier (UPID). You can supply up to 100 UPIDs.

taxid

Numeric: (optional) NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

keyword

Character: (optional) Limit the search to entries containing the keyword. See UniProt Keywords.

xref

Character: (optional) Proteome cross-references such as genome assembly ID or Biosample ID. You can supply up to 20 cross-reference IDs.

genome_acc

Character: (optional) Genome accession associated with the proteome's components. You can supply up to 20 accessions.

is_ref_proteome

Logical: (optional) If TRUE, return only reference proteomes; if FALSE, return only non-reference proteomes; if NULL, do not filter by this criterion. See 'What are reference proteomes?' for more information.

is_redundant

Logical: (optional) If TRUE, return only redundant proteomes; if FALSE, return only non-redundant proteomes; if NULL, do not filter by redundancy. See 'Reducing proteome redundancy' for more information.

...

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

Value

A list named by UPID. Each element contains one matching proteome's metadata.

Details

At least one search criterion is required.

Corresponding API Resources

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

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()

Examples

# \donttest{
rba_uniprot_proteomes_search(name = "SARS-CoV")
# }
# \donttest{
rba_uniprot_proteomes_search(genome_acc = "AY274119")
# }