biomcp MCP — 사용 사례, 설치 & 라이브 데모

왜 쓰나요

핵심 기능

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

라이브 데모

실제 사용 모습

biomcp.replay ▶ 준비됨

0/0

설치

클라이언트 선택

~/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
    }
  }
}

Claude Desktop → Settings → Developer → Edit Config 열기. 저장 후 앱 재시작.

~/.cursor/mcp.json · .cursor/mcp.json

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

Cursor는 Claude Desktop과 동일한 mcpServers 스키마 사용. 프로젝트 설정이 전역보다 우선.

VS Code → Cline → MCP Servers → Edit

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

Cline 사이드바의 MCP Servers 아이콘 클릭 후 "Edit Configuration" 선택.

~/.codeium/windsurf/mcp_config.json

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

Claude Desktop과 같은 형식. Windsurf 재시작 후 적용.

~/.continue/config.json

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

Continue는 맵이 아닌 서버 오브젝트 배열 사용.

~/.config/zed/settings.json

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

context_servers에 추가. 저장 시 Zed가 핫 리로드.

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

한 줄 명령. claude mcp list로 확인, claude mcp remove로 제거.

사용 사례

실전 활용법: biomcp

Triage a patient's gene variant for clinical relevance

👤 Genetic counselors, clinical researchers ⏱ ~15 min advanced

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

사전 조건

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

흐름

Look up the variant

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

→ Consolidated card from multiple sources
Pull supporting papers

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

→ Paper list with PMIDs
Check for trials

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

→ Trial list from ClinicalTrials.gov

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

함정

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

언제 쓸까: You need a bibliography on a specific gene-disease-drug angle.

흐름

Search articles

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

→ Deduplicated paper list
Summarize

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

→ Annotated bibliography

결과: A defensible starting bibliography.

함께 쓰기: filesystem

Check adverse-event profile for a drug

👤 Pharmacy, safety teams ⏱ ~20 min intermediate

언제 쓸까: Before recommending a drug, check OpenFDA / Drugs@FDA signals.

흐름

Query drug

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

→ Ranked AE table
Context

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

→ Label vs real-world comparison

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

Find clinical trials matching a patient profile

👤 Clinicians, patient advocates ⏱ ~25 min advanced

언제 쓸까: A patient exhausted standard options and you want to scan for trial matches.

흐름

Match trials

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

→ Trial list with NCT IDs
Summarize eligibility

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

→ Per-trial eligibility card

결과: A prioritized trial match list for clinical discussion.

조합

다른 MCP와 조합해 10배 효율

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.✓ 복사됨

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.✓ 복사됨

도구

이 MCP가 노출하는 것

도구	입력	언제 호출	비용
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

비용 및 제한

운영 비용

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

보안

권한, 시크릿, 파급범위

자격 증명 저장: Env vars per provider key

데이터 외부 송신: 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.

문제 해결

자주 발생하는 오류와 해결

Rate limited on PubMed

Set NCBI_API_KEY for higher limits.

확인: Check NCBI API Key page

OncoKB returns 403

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

확인: 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).

확인: Search on genecards.org

대안

biomcp 다른 것과 비교

대안	언제 쓰나	단점/장점
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

biomcp