Enables searching and retrieving biomedical literature from PubMed, including articles, reviews, and citations.
One command grammar. 50+ biomedical databases. Zero learning curve.
Genes, variants, drugs, trials, papers, pathways, phenotypes — all through a single MCP endpoint.
BioMCP is a production-grade Model Context Protocol server that unifies PubMed, ClinicalTrials.gov, ClinVar, gnomAD, OncoKB, Reactome, KEGG, UniProt, PharmGKB, CPIC, OpenFDA, CDC VAERS, Monarch Initiative, GWAS Catalog, DisGeNET, AlphaGenome, cBioPortal, and 40+ other biomedical sources behind one consistent read-only API.
# Option A: Pull from Docker Hub (recommended)
docker pull jackgucci/biomcp:latest
docker compose up -d
# Option B: Build from source
git clone https://github.com/gucci10248/JEFFREY.git && cd JEFFREY
cp .env.example .env
bash build.sh
docker compose up -d
# Test
curl http://localhost:8080/health # → {"status":"ok"}Your MCP server is live at http://localhost:8080/mcp.
Related MCP server: BioMCP
{
"mcpServers": {
"biomcp": {
"type": "streamableHttp",
"url": "http://localhost:8080/mcp"
}
}
}# ~/.hermes/config.yaml
mcp:
servers:
biomcp:
type: streamableHttp
url: http://localhost:8080/mcp
enabled: trueEndpoint: http://localhost:8080/mcpCommand | Example |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Command | Example |
|
|
|
|
|
|
|
|
Command | Example |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Command | Example |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Command | Example |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Command | Example |
|
|
|
|
|
|
|
|
|
|
Command | Example |
|
|
|
|
|
|
|
|
Command | Example |
|
|
|
|
Command | Example |
|
|
|
|
|
|
Command | Example |
|
|
|
|
|
|
Command | Example |
|
|
|
|
Command | Example |
|
|
|
|
Command | Example |
|
|
|
|
Command | Example |
| Check API connectivity |
| Print server version |
|
|
Source | Coverage |
PubMed | 36M+ biomedical citations |
Europe PMC | Full-text, preprints, patents |
ClinicalTrials.gov | 500K+ registered trials |
ClinVar | 3M+ variant-disease annotations |
gnomAD | Population allele frequencies |
OncoKB | Cancer variant clinical actionability |
OpenFDA | FDA drug/device adverse events |
UniProt | Protein function & structure |
KEGG | Metabolic & signaling pathways |
Reactome | Curated pathway database |
PharmGKB | Pharmacogenomics knowledge |
CPIC | Clinical pharmacogenetics guidelines |
Monarch Initiative | Cross-species phenotype ontology |
GWAS Catalog | Genome-wide association studies |
cBioPortal | Cancer genomics datasets |
DDInter | Drug-drug interaction database |
CDC VAERS | Vaccine adverse events |
EMA | European Medicines Agency data |
WHO Prequalification | Essential medicines quality |
NCBI GTR | Genetic testing registry |
AlphaGenome | Genomic variant predictions |
DisGeNET | Gene-disease associations |
Read-only by design — no mutations to external data sources, safe for production
Single command grammar — one pattern for all entity types, no learning curve
Resilient — multi-source fallback, degraded responses with transparent source status
Non-root container — runs as unprivileged biomcp user
Read-only root filesystem — docker compose enforces read_only: true
Minimal attack surface — single static binary, zero runtime dependencies
Zero telemetry — no outbound calls except to public biomedical APIs
SHA256-verified binary — build.sh verifies checksum from GitHub Releases
Auto-updating data caches — EMA, WHO, GTR feeds auto-refresh on stale detection
curl http://localhost:8080/health # → {"status":"ok"} — API connectivity
curl http://localhost:8080/readyz # → 200 — ready to serve traffic
curl http://localhost:8080/ # → Welcome page (HTML)Docker 24+ & Docker Compose v2
~200MB disk (image + data volumes)
Outbound internet access to public biomedical APIs
Optional: NCBI_API_KEY, S2_API_KEY, UNPAYWALL_EMAIL for higher rate limits
See SECURITY.md for vulnerability reporting and CODEOWNERS for maintainer contacts.
Apache License 2.0 — see LICENSE.
This server cannot be installed
Unclaimed servers have limited discoverability.
If you are the server author, to access and configure the admin panel.
MCP gateway federating 21 biomedical MCP servers behind one endpoint: gnomAD, ClinVar, HPO, VEP.
PubMed MCP — wraps the NCBI E-utilities API (biomedical literature, free, no auth)
Open Targets MCP — disease/target/drug knowledge graph.
We provide all the information about MCP servers via our MCP API.
curl -X GET 'https://glama.ai/api/mcp/v1/servers/gucci10248/JEFFREY'
If you have feedback or need assistance with the MCP directory API, please join our Discord server