Biomedical APIs MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| OPENFDA_API_KEY | No | Optional: increases OpenFDA rate limits | |
| CRUNCHBASE_API_KEY | No | Optional: enables Crunchbase free tier |
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_clinical_trialsB | Search ClinicalTrials.gov for registered trials by keyword or advanced filter |
| search_chembl_compoundsB | Search ChEMBL for small molecules by name or SMILES |
| get_chembl_activitiesC | Retrieve bioactivity data from ChEMBL by target or assay ID |
| get_pubchem_compoundC | Retrieve compound properties from PubChem by name |
| search_openfda_drug_eventsB | Search FDA adverse event reports by drug name or other criteria |
| search_europepmc_articlesC | Search Europe PMC for biomedical literature by keyword |
| query_dbgapC | NIH dbGaP genomic/clinical datasets (requires credentials) |
| query_physionetB | PhysioNet physiological signal datasets (requires credentials) |
| query_mimicC | MIMIC-IV ICU records (requires PhysioNet credential) |
| query_ukbiobankC | UK Biobank large-scale biomedical data (requires application) |
| query_drugbankC | DrugBank structured drug data (requires license) |
| query_bindingdbC | BindingDB measured binding affinities (bulk download available) |
| query_opentrialsD | OpenTrials merged trial data & sponsors (open access) |
| query_crunchbaseB | Crunchbase company & funding data (free tier limited) |
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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