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uniprot_database

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UniProt — protein sequence, function, taxonomy, cross-references. Search proteins by query, retrieve a UniProt entry, map IDs between databases (PDB↔UniProt etc.), pull FASTA sequence, fetch metadata, run SPARQL against sparql.uniprot.org. Use whenever the user mentions a UniProt accession (e.g. P04637), asks for protein function/sequence/family info, or needs cross-DB ID mapping. Don't use for AlphaFold structures (use alphafold_database) or PDB structures (use rcsb_database).

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UniProt Database

Overview

UniProt KnowledgeBase (UniProtKB) is the central protein-knowledge resource. This skill exposes 6 tools spanning text search, single-entry retrieval, ID mapping, sequence/metadata download, and SPARQL queries.

Project Tools (VenusFactory2)

ToolArgsReturnsDescription
download_uniprot_search_by_queryquery (UniProt query syntax, e.g. organism_id:9606 AND reviewed:true), out_path, optional formatrich JSON envelopeSearch UniProtKB; results saved to file.
download_uniprot_retrieve_by_iduniprot_id (e.g. P04637), out_path, optional frmt (fasta default)rich JSON envelopeRetrieve one entry in the chosen format.
download_uniprot_mappingfr (from db, e.g. PDB), to (to db, e.g. UniProtKB_AC-ID), query (comma-separated IDs), out_pathrich JSON envelopeCross-database ID mapping (PDB↔UniProt, gene name↔accession, etc.).
download_uniprot_seq_by_iduniprot_id, out_pathrich JSON envelope; FASTA fileSequence FASTA only.
download_uniprot_meta_by_iduniprot_id, out_pathrich JSON envelope; JSON fileFull metadata (function, taxonomy, GO, xrefs, etc.).
download_uniprot_sparql_by_queryquery (SPARQL string), out_dir (required), timeout (default 120s)rich JSON envelope; SPARQL JSON file at file_info.file_path; biological_metadata.row_count + head_varsRun an arbitrary SPARQL query against https://sparql.uniprot.org/sparql.

When to Use Which Tool

GoalTool
You have a UniProt accession, want sequencedownload_uniprot_seq_by_id
You have a UniProt accession, want everything elsedownload_uniprot_meta_by_id
You have a gene name / PDB ID, want UniProtdownload_uniprot_mapping
You have a free-text query, want a listdownload_uniprot_search_by_query
You need a complex cross-resource graph query (e.g. all enzymes in pathway X catalyzing reaction Y)download_uniprot_sparql_by_query

SPARQL Quick Examples

Top 5 proteins by name:

PREFIX up: <http://purl.uniprot.org/core/>
SELECT ?p ?name WHERE {
  ?p a up:Protein .
  ?p up:recommendedName / up:fullName ?name .
} LIMIT 5

Proteins in human, with a specific GO term:

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
SELECT ?protein ?name
WHERE {
  ?protein a up:Protein .
  ?protein up:organism taxon:9606 .
  ?protein up:classifiedWith <http://purl.obolibrary.org/obo/GO_0003700> .
  ?protein up:recommendedName / up:fullName ?name .
} LIMIT 20

Common Mistakes

  • Passing an unreviewed entry's accession when you need curated info: filter with reviewed:true in your search.
  • Mapping in the wrong direction: fr=PDB to=UniProtKB_AC-ID for "PDB → UniProt"; flip for the reverse.
  • SPARQL timeout on broad queries: add LIMIT N; default endpoint timeout is harsh. Bump timeout parameter if your query is legitimately heavy.

References