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 |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| 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 | |
TDQS
Scored across 14 tools
Each tool targets a distinct biomedical database or data type, with descriptions clearly differentiating their sources and functions. There is no overlapping purpose among the 14 tools.
Tool names follow a consistent verb_noun pattern: 'get_' for direct retrieval, 'query_' for credentialed databases, and 'search_' for keyword queries. The prefixes are used consistently across the set.
With 14 tools covering diverse biomedical data sources (compounds, activities, trials, literature, adverse events, clinical datasets), the count is well-scoped for the server's purpose without being excessive or thin.
The tool set covers major biomedical data domains, including compounds, bioactivities, trials, literature, and clinical datasets. Minor gaps exist (e.g., protein data, gene expression), but core workflows are well-supported.