| name | uniprot_database |
| description | 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). |
| license | Unknown |
| metadata | {"skill-author":"VenusFactory2."} |
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)
| Tool | Args | Returns | Description |
|---|
| download_uniprot_search_by_query | query (UniProt query syntax, e.g. organism_id:9606 AND reviewed:true), out_path, optional format | rich JSON envelope | Search UniProtKB; results saved to file. |
| download_uniprot_retrieve_by_id | uniprot_id (e.g. P04637), out_path, optional frmt (fasta default) | rich JSON envelope | Retrieve one entry in the chosen format. |
| download_uniprot_mapping | fr (from db, e.g. PDB), to (to db, e.g. UniProtKB_AC-ID), query (comma-separated IDs), out_path | rich JSON envelope | Cross-database ID mapping (PDB↔UniProt, gene name↔accession, etc.). |
| download_uniprot_seq_by_id | uniprot_id, out_path | rich JSON envelope; FASTA file | Sequence FASTA only. |
| download_uniprot_meta_by_id | uniprot_id, out_path | rich JSON envelope; JSON file | Full metadata (function, taxonomy, GO, xrefs, etc.). |
| download_uniprot_sparql_by_query | query (SPARQL string), out_dir (required), timeout (default 120s) | rich JSON envelope; SPARQL JSON file at file_info.file_path; biological_metadata.row_count + head_vars | Run an arbitrary SPARQL query against https://sparql.uniprot.org/sparql. |
When to Use Which Tool
| Goal | Tool |
|---|
| You have a UniProt accession, want sequence | download_uniprot_seq_by_id |
| You have a UniProt accession, want everything else | download_uniprot_meta_by_id |
| You have a gene name / PDB ID, want UniProt | download_uniprot_mapping |
| You have a free-text query, want a list | download_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
