MCP server
by genomoncology
BioMCP integrates ClinicalTrials.gov, PubMed, and MyVariant.info for unified biomedical database access with structured,
Queries biomedical databases like PubMed, ClinicalTrials.gov, and genetic variant databases through a unified command interface. Provides structured access to research articles, clinical trials, genes, variants, drugs, and diseases with cross-referencing capabilities.
BioMCP (Biomedical Database Integration) is an official MCP server published by genomoncology that provides AI assistants with tools and capabilities via the Model Context Protocol. BioMCP integrates ClinicalTrials.gov, PubMed, and MyVariant.info for unified biomedical database access with structured, It is categorized under databases, analytics data.
You can install BioMCP (Biomedical Database Integration) in your AI client of choice. Use the install panel on this page to get one-click setup for Cursor, Claude Desktop, VS Code, and other MCP-compatible clients. This server runs locally on your machine via the stdio transport.
MIT
BioMCP (Biomedical Database Integration) is released under the MIT license. This is a permissive open-source license, meaning you can freely use, modify, and distribute the software.
Enable Claude to query your database directly using natural language
Example
Ask 'Show me top 10 customers by revenue this month' and get SQL results instantly
Eliminate manual SQL writing for ad-hoc queries, get insights 10x faster
Generate complex reports and analytics without leaving conversation
Example
Analyze sales trends, cohort retention, user behavior patterns conversationally
Democratize data access—non-technical team members can query databases
Understand database structure, relationships, and data models
Example
'Explain the user_orders table schema and its relationships'
Onboard engineers faster, explore unfamiliar databases efficiently
Share your MCP server with the developer community
BioMCP (Biomedical Database Integration) is a well-scoped MCP server in the explainx.ai directory — install snippets and categories matched our Claude Code setup.
BioMCP (Biomedical Database Integration) has been reliable for tool-calling workflows; the MCP profile page is a good permalink for internal docs.
BioMCP (Biomedical Database Integration) is a well-scoped MCP server in the explainx.ai directory — install snippets and categories matched our Claude Code setup.
We evaluated BioMCP (Biomedical Database Integration) against two servers with overlapping tools; this profile had the clearer scope statement.
BioMCP (Biomedical Database Integration) reduced integration guesswork — categories and install configs on the listing matched the upstream repo.
I recommend BioMCP (Biomedical Database Integration) for teams standardizing on MCP; the explainx.ai page compares cleanly with sibling servers.
BioMCP (Biomedical Database Integration) is among the better-indexed MCP projects we tried; the explainx.ai summary tracks the official description.
Strong directory entry: BioMCP (Biomedical Database Integration) surfaces stars and publisher context so we could sanity-check maintenance before adopting.
BioMCP (Biomedical Database Integration) is among the better-indexed MCP projects we tried; the explainx.ai summary tracks the official description.
We wired BioMCP (Biomedical Database Integration) into a staging workspace; the listing’s GitHub and npm pointers saved time versus hunting across READMEs.
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BioMCP is a single-binary CLI and MCP server for querying biomedical databases. One command grammar, compact markdown output, 12 entities across 15+ data sources.
uv tool install biomcp-cli
# or: pip install biomcp-cli
This installs the biomcp binary on your PATH.
curl -fsSL https://biomcp.org/install.sh | bash
Install guided investigation workflows into your agent directory:
biomcp skill install ~/.claude --force
{
"mcpServers": {
"biomcp": {
"command": "biomcp",
"args": ["serve"]
}
}
}
cargo build --release --locked
biomcp health --apis-only # verify API connectivity
biomcp list # show all entities and commands
biomcp list gene # show gene-specific filters and examples
search <entity> [filters] → discovery
get <entity> <id> [sections] → focused detail
<entity> <helper> <id> → cross-entity pivots
enrich <GENE1,GENE2,...> → gene-set enrichment
batch <entity> <id1,id2,...> → parallel gets
| Entity | Sources | Example |
|---|---|---|
| gene | MyGene.info, UniProt, Reactome, QuickGO, STRING, CIViC | biomcp get gene BRAF pathways |
| variant | MyVariant.info, ClinVar, gnomAD, CIViC, OncoKB, cBioPortal, GWAS Catalog, AlphaGenome | biomcp get variant "BRAF V600E" clinvar |
| article | PubMed, PubTator3, Europe PMC | biomcp search article -g BRAF --limit 5 |
| trial | ClinicalTrials.gov, NCI CTS API | biomcp search trial -c melanoma -s recruiting |
| drug | MyChem.info, ChEMBL, OpenTargets, Drugs@FDA, CIViC | biomcp get drug pembrolizumab targets |
| disease | Monarch Initiative, MONDO, CIViC, OpenTargets | biomcp get disease "Lynch syndrome" genes |
| pathway | Reactome, g:Profiler | biomcp get pathway R-HSA-5673001 genes |
| protein | UniProt, InterPro, STRING, PDB/AlphaFold | biomcp get protein P15056 domains |
| adverse-event | OpenFDA (FAERS, MAUDE, Recalls) | biomcp search adverse-event -d pembrolizumab |
| pgx | CPIC, PharmGKB | biomcp get pgx CYP2D6 recommendations |
| gwas | GWAS Catalog | biomcp search gwas --trait "type 2 diabetes" |
| phenotype | Monarch Initiative (HPO) | biomcp search phenotype "HP:0001250" |
Pivot between related entities without rebuilding filters:
biomcp variant trials "BRAF V600E" --limit 5
biomcp variant articles "BRAF V600E"
biomcp drug adverse-events pembrolizumab
biomcp drug trials pembrolizumab
biomcp disease trials melanoma
biomcp disease drugs melanoma
biomcp disease articles "Lynch syndrome"
biomcp gene trials BRAF
biomcp gene drugs BRAF
biomcp gene articles BRCA1
biomcp gene pathways BRAF
biomcp pathway drugs R-HSA-5673001
biomcp pathway articles R-HSA-5673001
biomcp pathway trials R-HSA-5673001
biomcp protein structures P15056
biomcp article entities 22663011
biomcp enrich BRAF,KRAS,NRAS --limit 10
Every get command supports selectable sections for focused output:
biomcp get gene BRAF # summary card
biomcp get gene BRAF pathways # add pathway section
biomcp get gene BRAF civic interactions # multiple sections
biomcp get gene BRAF all # everything
biomcp get variant "BRAF V600E" clinvar population conservation
biomcp get drug pembrolizumab label targets civic approvals
biomcp get disease "Lynch syndrome" genes phenotypes variants
biomcp get trial NCT02576665 eligibility locations outcomes
Most commands work without credentials. Optional keys improve rate limits:
export NCBI_API_KEY="..." # PubTator, PMC OA, NCBI ID converter
export OPENFDA_API_KEY="..." # OpenFDA rate limits
export NCI_API_KEY="..." # NCI CTS trial search (--source nci)
export ONCOKB_TOKEN="..." # OncoKB variant helper
export ALPHAGENOME_API_KEY="..." # AlphaGenome variant effect prediction
BioMCP rate limiting is process-local. For many concurrent workers, run one shared
biomcp serve-http endpoint so all workers share a single limiter budget:
biomcp serve-http --host 0.0.0.0 --port 8080
14 guided investigation workflows are built in:
biomcp skill list
biomcp skill show 03
| # | Skill | Focus |
|---|---|---|
| 01 | variant-to-treatment | Variant annotation to treatment options |
| 02 | drug-investigation | Drug mechanism, safety, alternatives |
| 03 | trial-searching | Trial discovery and patient matching |
| 04 | rare-disease | Rare disease evidence and trial strategy |
| 05 | drug-shortages | Shortage monitoring and alternatives |
| 06 | advanced-therapies | CAR-T and checkpoint therapy workflows |
| 07 | hereditary-cancer | Hereditary cancer syndrome workup |
| 08 | resistance | Resistance mechanisms and next-line options |
| 09 | gene-function-lookup | Gene-centric function and context |
| 10 | gene-set-analysis | Enrichment, pathway, and interaction synthesis |
| 11 | literature-synthesis | Evidence synthesis with cross-entity checks |
| 12 | pharmacogenomics | PGx gene-drug interactions and dosing |
| 13 | phenotype-triage | Symptom-first rare disease workup |
| 14 | protein-pathway | Protein structure and pathway deep dive |
biomcp version # show version and build info
biomcp health # check all API connectivity
biomcp update # self-update to latest release
biomcp update --check # check for updates without installing
biomcp uninstall # remove biomcp from ~/.local/bin
Full documentation at biomcp.org.
MIT
Run data quality queries to catch anomalies and inconsistencies
Example
Find duplicate records, missing values, orphaned foreign keys automatically
Maintain data integrity with less manual SQL work
Prerequisites
Time Estimate
15-30 minutes including configuration and testing
Steps
Troubleshooting
✓ Do
✗ Don't
💡 Pro Tips
Architecture
MCP server acts as bridge between Claude and database, translating natural language to SQL queries and returning results in structured format.
Protocols
Compatibility
✓ Use when
Use for ad-hoc data queries, exploratory analysis, report generation, schema exploration, and democratizing data access. Best for read-heavy analytics workloads.
✗ Avoid when
Avoid for production write operations, mission-critical transactions, real-time OLTP workloads, or when database contains sensitive PII without proper access controls. Use read replicas, not primary.