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Search UniProt entries

Source: R/uniprot_proteins.R
rba_uniprot_proteins_search.Rd

Search and retrieve UniProt Knowledgebase (UniProtKB) protein entries by accession, annotation, gene, organism, sequence properties, or other supported criteria.

Usage

rba_uniprot_proteins_search(
  accession = NULL,
  reviewed = NULL,
  isoform = NULL,
  go_term = NULL,
  keyword = NULL,
  ec = NULL,
  gene = NULL,
  exact_gene = NULL,
  protein = NULL,
  organism = NULL,
  taxid = NULL,
  pubmed = NULL,
  seq_length = NULL,
  md5 = NULL,
  ...
)

Arguments

accession

Character: (optional) UniProtKB primary or secondary accession(s). You can supply up to 100 accession numbers.

reviewed

Logical: (optional) If TRUE, return only reviewed Swiss-Prot entries. If FALSE, return only unreviewed TrEMBL entries. This is a refining filter and cannot be the sole search criterion.

isoform

Numeric: (optional) One of:

  • 0: Exclude isoforms; this only refines another criterion.

  • 1: Return isoforms only; this can be a stand-alone criterion.

  • 2: Return canonical entries and isoforms; this only refines another criterion.

See alternative products.

go_term

Character: (optional) Limit the search to entries associated with your supplied GO (Gene Ontology) term. Supply either a GO ID or a character string partially or fully matching the term, e.g. "GO:0001776" or "leukocyte homeostasis". If you supply "leukocyte", any term containing that word will be included, e.g. "leukocyte chemotaxis" or "leukocyte activation".

keyword

Character: (optional) Limit the search to entries that contain your supplied keyword. See UniProt Keywords.

ec

Character: (optional) EC (Enzyme Commission) number(s). You can supply up to 20 EC numbers.

gene

Character: (optional) UniProt gene name(s). You can supply up to 20 gene names. For example, if you supply "CD40", "CD40 ligand" will also be included.

exact_gene

Character: (optional) UniProt exact gene name(s). You can supply up to 20 exact gene names. For example, if you supply "CD40", "CD40 ligand" will not be included in the results.

protein

Character: (optional) UniProt protein name.

organism

Character: (optional) Organism name.

taxid

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

pubmed

Character or Numeric: (optional) PubMed ID(s) cited by the returned entries. You can supply up to 20 IDs.

seq_length

Character or Numeric: (optional) An exact sequence length (e.g. 150) or a range of sequence lengths (e.g. "130-158").

md5

Character: (optional) A 32-character hexadecimal sequence MD5 checksum.

...

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

Value

A list named by UniProt accession. Each element contains one matching UniProtKB entry.

Details

At least one primary search criterion is required. The value isoform = 1 can be used by itself; reviewed and the other isoform values only refine another criterion.

UniProtKB entries are grouped into two sections:

  1. Reviewed (Swiss-Prot): Manually annotated records with information extracted from literature and curator-evaluated computational analysis.

  2. Unreviewed (TrEMBL): Computationally analyzed records that await full manual annotation.

Corresponding API Resources

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

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 - Proteins": rba_uniprot_proteins(), rba_uniprot_proteins_crossref()

Examples

# \donttest{
rba_uniprot_proteins_search(accession = "Q99616")
# }
# \donttest{
rba_uniprot_proteins_search(gene = "cd40")
# }
# \donttest{
rba_uniprot_proteins_search(gene = "cd40 ligand")
# }
# \donttest{
rba_uniprot_proteins_search(gene = "cd40",  reviewed = TRUE)
# }
# \donttest{
rba_uniprot_proteins_search(gene = "cd40",  reviewed = TRUE, isoform = 1)
# }
# \donttest{
rba_uniprot_proteins_search(
  keyword = "Inhibition of host chemokines by virus"
)
# }
# \donttest{
rba_uniprot_proteins_search(keyword = "chemokines")
# }