UniProt
UniProt is the protein sequence and function knowledgebase of the UniProt Consortium. Its UniProtKB entries carry a protein's name, function notes and links to gene databases. Through ScholarMuse, an agent calls lookup_gene_protein with a gene symbol, protein name or UniProt accession and gets the accession, protein name, length and function text, with reviewed Swiss-Prot entries preferred.
ScholarMuse tools: lookup_gene_protein. Each successful call uses credits.
Ask your agent
What your agent gets back
Every record carries id, source, title, url, license, attribution and retrievedAt. The fields below are the data that comes from UniProt.
lookup_gene_protein
The tool returns one merged record. These are the parts filled from UniProt. Field names are paths inside `data`.
- ids.uniprot
- UniProtKB accession
- proteinName
- Recommended protein name
- proteinLength
- Sequence length in amino acids
- function
- Function comment text, cut at 2,000 characters
- uniprotReviewed
- True for a reviewed Swiss-Prot entry
- aliases
- Gene synonyms, used when NCBI Gene gives none
- links.uniprot
- URL of the entry at UniProt
What it covers
- UniProtKB entries, both reviewed (Swiss-Prot) and unreviewed. A reviewed entry is tried first and uniprotReviewed says which kind was used.
- Lookup by UniProt accession, by exact gene symbol in one organism, by protein name, or by Ensembl gene id.
- UniProt's cross-references to NCBI Gene and Ensembl decide which gene records are attached to the answer.
Limits
- One protein per call. The amino acid sequence itself is not returned, only its length.
- Only the function comment is returned, cut at 2,000 characters. Features, isoforms, variants, subcellular location and references are not.
- When a gene has several UniProtKB entries, one is chosen (reviewed first), so other entries for the same gene are not listed.
- If the accession belongs to a different organism than the one requested, the organism of the UniProt entry is used for the rest of the lookup.
How ScholarMuse reaches UniProt
The connector calls the UniProt REST API at rest.uniprot.org/uniprotkb directly: an entry fetch for an accession, or a search by exact gene name, protein name or Ensembl cross-reference. No API key is sent.
Entries fetched by accession are cached for up to 7 days and searches for up to 1 day, so recent UniProt updates can take that long to appear.
API key: the upstream API can be called without one, so you do not add one.
Licence and attribution
Licence: CC BY 4.0
Protein data from UniProt (uniprot.org), UniProt Consortium, CC BY 4.0.
Records that come from UniProt carry this licence and attribution. When you cite the data in a paper, follow UniProt's own citation guidance.
