MCP Tools Reference#

The BDP MCP server exposes 24 tools across 10 categories. All tools query the live knowledge graph and return structured JSON.

Genes#

| Tool | Description | |---|---| | get_gene | Look up a gene by symbol, Ensembl ID, or Entrez ID | | get_gene_interactions | Protein-protein interactions (STRING) | | get_gene_variants | Clinically relevant variants (ClinVar) | | get_gene_literature | Publications mentioning the gene (PubMed / Europe PMC) | | get_gene_pathways | Pathways containing the gene (Reactome) | | get_gene_diseases | Diseases associated with the gene | | get_gene_drugs | Drugs targeting the gene |

Diseases#

| Tool | Description | |---|---| | get_disease | Look up a disease by name or MONDO ID | | get_disease_phenotypes | HPO phenotypes for a disease | | get_disease_genes | Genes associated with a disease | | get_disease_trials | Clinical trials for a disease (ClinicalTrials.gov) |

Drugs#

| Tool | Description | |---|---| | get_drug | Look up a drug by name or identifier | | get_drug_indications | Approved and investigational indications | | get_drug_adverse_events | Adverse event signals (OpenFDA FAERS) |

Compounds#

| Tool | Description | |---|---| | get_compound | Look up a chemical compound (ChEBI / ChEMBL) | | get_compound_targets | Protein targets for a compound |

Pathways#

| Tool | Description | |---|---| | get_pathway | Look up a biological pathway (Reactome) | | get_pathway_proteins | Proteins participating in a pathway |

Phenotypes#

| Tool | Description | |---|---| | get_phenotype | Look up an HPO phenotype term | | get_phenotype_diseases | Diseases associated with a phenotype |

Literature#

| Tool | Description | |---|---| | search_literature | Full-text search across PubMed and Europe PMC | | get_publication | Retrieve a publication by PMID or DOI |

Structures#

| Tool | Description | |---|---| | get_structure | Retrieve a PDB structure by ID | | get_protein_structures | PDB structures for a UniProt protein (SIFTS) |

Semantic Search#

| Tool | Description | |---|---| | semantic_search | Vector-similarity search across the knowledge graph |

Graph Traversal#

| Tool | Description | |---|---| | traverse | Multi-hop traversal: follow relationships across entity types |

Usage Notes#

• All identifiers are resolved automatically — pass a gene symbol, MONDO ID, UniProt accession, PMID, etc.
• Results are paginated; use limit and offset parameters for large result sets
• Tools return structured JSON suitable for further agent reasoning

See MCP Overview for setup instructions.