biomcp MCP — Casos de uso, Instalar & Demo ao vivo

Por que usar

Principais recursos

11+ entity types covering genes, variants, articles, trials, drugs, diseases, pathways, proteins, adverse events, pharmacogenomics, GWAS
Deduplication across overlapping sources (PubTator3)
Optional API keys unlock higher rate limits and premium data (NCBI, OncoKB, Semantic Scholar, NCI, OpenFDA)
Install via curl script, PyPI (biomcp-cli), or remote HTTP
Zero-key operation possible — unauthenticated public APIs work by default

Demo ao vivo

Como fica na prática

biomcp.replay ▶ pronto

0/0

Instalar

Escolha seu cliente

~/Library/Application Support/Claude/claude_desktop_config.json · Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "biomcp": {
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ],
      "_inferred": true
    }
  }
}

Abra Claude Desktop → Settings → Developer → Edit Config. Reinicie após salvar.

~/.cursor/mcp.json · .cursor/mcp.json

{
  "mcpServers": {
    "biomcp": {
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ],
      "_inferred": true
    }
  }
}

Cursor usa o mesmo esquema mcpServers que o Claude Desktop. Config de projeto vence a global.

VS Code → Cline → MCP Servers → Edit

{
  "mcpServers": {
    "biomcp": {
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ],
      "_inferred": true
    }
  }
}

Clique no ícone MCP Servers na barra lateral do Cline, depois "Edit Configuration".

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "biomcp": {
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ],
      "_inferred": true
    }
  }
}

Mesmo formato do Claude Desktop. Reinicie o Windsurf para aplicar.

~/.continue/config.json

{
  "mcpServers": [
    {
      "name": "biomcp",
      "command": "TODO",
      "args": [
        "See README: https://github.com/genomoncology/biomcp"
      ]
    }
  ]
}

O Continue usa um array de objetos de servidor em vez de um map.

~/.config/zed/settings.json

{
  "context_servers": {
    "biomcp": {
      "command": {
        "path": "TODO",
        "args": [
          "See README: https://github.com/genomoncology/biomcp"
        ]
      }
    }
  }
}

Adicione em context_servers. Zed recarrega automaticamente ao salvar.

claude mcp add biomcp -- TODO 'See README: https://github.com/genomoncology/biomcp'

Uma linha só. Verifique com claude mcp list. Remova com claude mcp remove.

Casos de uso

Usos do mundo real: biomcp

Triage a patient's gene variant for clinical relevance

👤 Genetic counselors, clinical researchers ⏱ ~15 min advanced

Quando usar: A VCF annotation returned a variant you've never seen — is it actionable?

Pré-requisitos

biomcp installed — curl -fsSL https://biomcp.org/install.sh | bash

Fluxo

Look up the variant

Look up BRCA2 c.7934del. ClinVar significance, gnomAD frequency, and any CIViC evidence.✓ Copiado

→ Consolidated card from multiple sources
Pull supporting papers

Find the 3 most cited PubMed articles on this variant.✓ Copiado

→ Paper list with PMIDs
Check for trials

Any open clinical trials recruiting for BRCA2 mutation carriers?✓ Copiado

→ Trial list from ClinicalTrials.gov

Resultado: A multi-source picture of a variant with evidence pointers.

Armadilhas

Not a substitute for clinical review — Always have a qualified clinician review — this is research aid, not diagnosis
Some sources disagree on variant classification — Surface disagreements explicitly; don't average them

Conduct a targeted literature review

👤 PhD students, MDs, industry researchers ⏱ ~20 min intermediate

Quando usar: You need a bibliography on a specific gene-disease-drug angle.

Fluxo

Search articles

Search PubMed + Europe PMC for 'KRAS G12C AND adagrasib' 2022-2026. Dedupe across sources.✓ Copiado

→ Deduplicated paper list
Summarize

For the top 10 by citation count, give me title + one-line take-home.✓ Copiado

→ Annotated bibliography

Resultado: A defensible starting bibliography.

Combine com: filesystem

Check adverse-event profile for a drug

👤 Pharmacy, safety teams ⏱ ~20 min intermediate

Quando usar: Before recommending a drug, check OpenFDA / Drugs@FDA signals.

Fluxo

Query drug

For pembrolizumab: top adverse events per OpenFDA FAERS, last 5 years, broken down by seriousness.✓ Copiado

→ Ranked AE table
Context

What's the expected AE profile per the FDA label vs FAERS real-world?✓ Copiado

→ Label vs real-world comparison

Resultado: Grounded safety picture combining label and post-market data.

Find clinical trials matching a patient profile

👤 Clinicians, patient advocates ⏱ ~25 min advanced

Quando usar: A patient exhausted standard options and you want to scan for trial matches.

Fluxo

Match trials

Find Phase 2/3 recruiting trials for stage IV NSCLC with EGFR exon 20 insertion, US sites.✓ Copiado

→ Trial list with NCT IDs
Summarize eligibility

For the top 5, summarize key inclusion/exclusion criteria.✓ Copiado

→ Per-trial eligibility card

Resultado: A prioritized trial match list for clinical discussion.

Combinações

Combine com outros MCPs para 10× de alavancagem

biomcp + filesystem

Save evidence memos as local markdown

For variant BRCA2 c.7934del, generate a one-page evidence memo and save to ~/research/brca2-7934.md.✓ Copiado

biomcp + documentation-server

Build a personal literature library across biomcp queries

Every paper I star via biomcp, also ingest into documentation-server for future RAG queries.✓ Copiado

Ferramentas

O que este MCP expõe

Ferramenta	Entradas	Quando chamar	Custo
gene	symbol or id, sources?: str[]	Gene-level lookup	multiple upstream calls
variant	hgvs\|rsid\|position	Variant interpretation	multiple upstream calls
article	query or pmid	Literature search	PubMed/Europe PMC/S2 calls
trial	query/condition/phase/status	Clinical trial match	CT.gov + NCI CTS calls
drug	name or id	Drug profile	multiple calls
disease	name or MONDO id	Disease context	multiple calls
adverse_event	drug or reaction	Safety analysis	OpenFDA calls

Custo e limites

O que custa rodar

Cota de API: Public APIs default. Optional keys raise limits: NCBI_API_KEY, S2_API_KEY, ONCOKB_TOKEN, OPENFDA_API_KEY, NCI_API_KEY
Tokens por chamada: Consolidated entity responses 1-5k tokens
Monetário: Free; some premium sources (OncoKB clinical) require license even with key
Dica: For heavy literature work, get NCBI_API_KEY (free) — triples PubMed rate.

Segurança

Permissões, segredos, alcance

Armazenamento de credenciais: Env vars per provider key

Saída de dados: Calls to biomedical public APIs; queries themselves can be sensitive (patient variants etc.)

Queries can include PHI-adjacent data — confirm your deployment's data handling before running on real patient info.
Not a medical device; outputs are research aids only.

Solução de problemas

Erros comuns e correções

Rate limited on PubMed

Set NCBI_API_KEY for higher limits.

Verificar: Check NCBI API Key page

OncoKB returns 403

OncoKB requires a token; register at oncokb.org and set ONCOKB_TOKEN.

Verificar: curl -H 'Authorization: Bearer $ONCOKB_TOKEN' https://www.oncokb.org/api/v1/utils/numbers

No results for a known gene symbol

Some symbols have aliases; try both (e.g. ERBB2 vs HER2).

Verificar: Search on genecards.org

Alternativas

biomcp vs. outros

Alternativa	Quando usar	Troca
Individual databases via direct REST	You only need one source	No deduplication or cross-linking
OpenTargets Platform directly	You primarily care about target-disease evidence	Narrower coverage

Mais

Recursos

📖 Leia o README oficial no GitHub

🐙 Ver issues abertas

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