BioMCP
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| S2_API_KEY | No | Semantic Scholar API key to prevent 429 rate limits | |
| NCI_API_KEY | No | NCI Clinical Trials API | |
| NCBI_API_KEY | No | NCBI API key for higher PubMed/NCBI rate limits | |
| ONCOKB_TOKEN | No | OncoKB cancer variant annotations | |
| UMLS_API_KEY | No | UMLS terminology services | |
| OPENFDA_API_KEY | No | OpenFDA API access | |
| DISGENET_API_KEY | No | DisGeNET disease-gene associations | |
| ALPHAGENOME_API_KEY | No | AlphaGenome variant scores |
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| gene_searchB | Search for genes by symbol, name, or keyword |
| gene_getC | Get detailed gene information by symbol |
| gene_diseasesA | Get diseases associated with a gene. Requires DISGENET_API_KEY environment variable for DisGeNET data; falls back to OpenTargets gene-disease associations when unavailable. |
| gene_drugsB | Find drugs targeting a gene |
| gene_trialsA | Find clinical trials for a gene |
| gene_articlesB | Find articles about a gene |
| gene_enrichA | Perform pathway enrichment analysis for a gene list |
| variant_searchA | Search for variants. Use structured parameters for best results:
|
| variant_getA | Get detailed variant information with optional sections. Core data (id, gene, rsid, significance) is always returned at the top level. Use sections to request additional data. |
| variant_oncokbA | Get OncoKB annotations for a variant in a cancer gene. Requires ONCOKB_TOKEN environment variable. |
| variant_trialsB | Find clinical trials for a variant |
| drug_searchC | Search for drugs by name, mechanism, or keyword |
| drug_getA | Get detailed drug information by name |
| drug_trialsA | Find clinical trials for a drug |
| disease_searchB | Search for diseases by name, phenotype, or keyword |
| disease_getA | Get detailed disease information by ID |
| disease_drugsA | Get drugs for a disease via OpenTargets |
| disease_trialsB | Get clinical trials for a disease |
| article_searchA | Search literature across multiple backends with federated search and deduplication |
| article_getA | Get article by PMID/PMCID/DOI. Citation: fast mode (~4s, auto-fallback to PubMed) or full mode (~15-30s, all 5 providers). Provider coverage depends on ID type. |
| trial_searchB | Search clinical trials by condition, intervention, or keyword |
| trial_getA | Get detailed trial information by NCT ID |
| discoverC | Free-text concept resolution - find entities matching a free-text query |
| batch_getB | Get multiple entities in parallel |
| pdbA | Access the Protein Data Bank (RCSB PDB) for macromolecular structure data. SEARCH: Provide "query" to find structures (e.g., "kinase inhibitor", "hemoglobin"). GET: Provide "pdb_id" to retrieve entry metadata with optional detail sections. DOWNLOAD: Provide "pdb_id" + download=true to save the structure file and get the file path. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
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