biocontext-knowledge-queries
BioContext Knowledge Queries
Use this skill when the user wants to look up gene/protein annotations, query pathway databases, find cell type markers, search biomedical literature, or explore drug-disease associations. BioContext provides programmatic access to 49 biomedical databases through a unified Python API.
This is a knowledge integration layer — use it to annotate analysis results (e.g., annotate DEG lists with protein function, find pathways for gene clusters, validate marker genes against PanglaoDB).
Available Functions by Category
Protein & Genomics
| Function | Database | Returns |
|---|---|---|
query_uniprot(gene_symbol, species) |
UniProt | Protein function, domains, GO terms, references |
get_uniprot_id(protein_symbol, species) |
UniProt | UniProt accession ID |
query_alphafold(protein_symbol, species) |
AlphaFold | Predicted 3D structure, confidence scores |
get_ensembl_id(gene_symbol, species) |
Ensembl | Ensembl gene ID (ENSG...) |
query_interpro(protein_id, source_db) |
InterPro | Protein domains, families, structural info |
search_interpro(query, entry_type) |
InterPro | Domain search by keyword |
query_string(protein_symbol, species, min_score) |
STRING | Protein-protein interactions |
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