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◇MCP serverHealthcareFree

BioMCP

Unified MCP access to biomedical literature, clinical trials, genes, variants, and drugs.

@ai-supply
Installs1.6k
↗ Source repository
← More HealthcareHealthcare leaderboard →How we grade security →Source ↗

BioMCP

BioMCP is a Model Context Protocol server that gives AI assistants and researchers unified access to trusted biomedical data sources through a single command grammar.

One query can fan out across biomedical literature (PubTator3 and Europe PMC, with an optional Semantic Scholar leg) and pivot between genes, variants, drugs, diseases, pathways, proteins, and articles, plus clinical-trial and variant databases — returning compact, evidence-oriented results over live public data with local study analytics.

It is intended for researchers, clinicians, and agents who need to search and cross-reference biomedical evidence without rebuilding a workflow for each source.

Rating rank
#1
of 11 in Healthcare
Install rank
#10
of 11 in Healthcare
Security score
100/100 · A
safe
Security rank
#1
of 11 in Healthcare
Installs
1.6k
cat avg 63k
This listing vs category average
Installs
this
cat avg
Security (of 100)
this
cat avg
Adoption trend
See the Healthcare leaderboard →
✓ Security: Safe · 100100/100 · grade Ascanned 2h ago

Only compromise signals — malicious or tampered code (leaked secrets, backdoors, path traversal, a dropped executable) — reduce the score. Dangerous-by-capability traits (shell, network, injection strings, pickle) are shown as risk surface: expected for some capabilities — a security tool ships offensive code on purpose — so they do not sink the grade.

Compromise signals
None — no malicious or tampered code detected in the scanned source.
What this capability can do · med confidence (static)
⚑ filesystem⚑ shell⚑ network⚑ secrets
egress → biomcp.org, ftp.ncbi.nlm.nih.gov, extranet.who.int, api.fda.gov, eutils.ncbi.nlm.nih.gov, wsearch.nlm.nih.gov, monarchinitiative.org, platform.opentargets.org +32
Risk surface (50)
External endpoints declaredlowgenomoncology-biomcp-ba4d160/.claude-plugin/marketplace.json
3 distinct host(s)
Embedded credentialshighexpected for this capabilitygenomoncology-biomcp-ba4d160/.github/workflows/release.yml
found: credentials in URL
Broad capability surfacelowgenomoncology-biomcp-ba4d160/.github/workflows/release.yml
3 high-impact capability categories referenced — verify least-privilege
External endpoints declaredlowgenomoncology-biomcp-ba4d160/.github/workflows/release.yml
1 distinct host(s)
Prompt-injection phrasinghighgenomoncology-biomcp-ba4d160/CHANGELOG.md
instruction-subversion language detected
External endpoints declaredlowgenomoncology-biomcp-ba4d160/CITATION.cff
2 distinct host(s)
Suspicious code patternshighgenomoncology-biomcp-ba4d160/Dockerfile
destructive rm -rf /
Suspicious code patternshighgenomoncology-biomcp-ba4d160/README.md
pipe-to-shell install
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/README.md
raw IP URL (6 URLs)
Egress to a private/loopback hosthighgenomoncology-biomcp-ba4d160/README.md
127.0.0.1
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/RUN.md
raw IP URL (3 URLs)
Potentially unbounded loopmediumgenomoncology-biomcp-ba4d160/architecture/experiments/24-diagnostic-entity-landscape/scripts/diagnostic_landscape/landscape.py
an infinite loop (while True / while(1) / for(;;)) may cause runaway consumption
External endpoints declaredlowgenomoncology-biomcp-ba4d160/architecture/experiments/24-diagnostic-entity-landscape/scripts/diagnostic_landscape/probes.py
4 distinct host(s)
Suspicious code patternsmediumgenomoncology-biomcp-ba4d160/architecture/experiments/243-architecture-hpo-phenotype-enrichment-for-clinical-symptoms/scripts/clinical_features_spike/reports.py
OS command execution
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/architecture/experiments/243-architecture-hpo-phenotype-enrichment-for-clinical-symptoms/scripts/curated_source_landscape.py
12 distinct host(s)
Path traversal sequencesmediumgenomoncology-biomcp-ba4d160/architecture/experiments/244-obsidian-vault-knowledge-base-with-pdf-to-markdown/harden.md
'../' present in content or name
Broad capability surfacelowgenomoncology-biomcp-ba4d160/architecture/experiments/244-obsidian-vault-knowledge-base-with-pdf-to-markdown/scripts/run_all_probes.py
4 high-impact capability categories referenced — verify least-privilege
External endpoints declaredlowgenomoncology-biomcp-ba4d160/architecture/experiments/244-obsidian-vault-knowledge-base-with-pdf-to-markdown/scripts/run_all_probes.py
9 distinct host(s)
External endpoints declaredlowgenomoncology-biomcp-ba4d160/architecture/experiments/245-biomedical-news-discovery-and-personalized-briefing/exploit.md
6 distinct host(s)
External endpoints declaredlowgenomoncology-biomcp-ba4d160/architecture/experiments/245-biomedical-news-discovery-and-personalized-briefing/source_registry.json
7 distinct host(s)
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/architecture/experiments/369-score-variant-agent-source-apis/lib/source_api_scoring/external_apis.py
15 distinct host(s)
External endpoints declaredlowgenomoncology-biomcp-ba4d160/architecture/experiments/variant-structure-annotation/variant_structure_annotation/sources.py
5 distinct host(s)
External endpoints declaredlowgenomoncology-biomcp-ba4d160/docs/getting-started/api-keys.md
8 distinct host(s)
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/docs/reference/data-sources.md
47 distinct host(s)
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/docs/reference/source-licensing.md
56 distinct host(s)
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/docs/reference/source-versioning.md
48 distinct host(s)
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/examples/rmcp_streamable_http_contract.rs
raw IP URL (1 URLs)
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/examples/streamable-http/README.md
raw IP URL (2 URLs)
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/scripts/contract-smoke.sh
16 distinct host(s)
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/scripts/release-smoke.sh
raw IP URL (4 URLs)
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/scripts/source-contracts.md
14 distinct host(s)
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/spec/fixtures/setup-article-fulltext-source-fixture.sh
raw IP URL (34 URLs)
Embedded credentialshighexpected for this capabilitygenomoncology-biomcp-ba4d160/spec/surface/discover.md
found: hardcoded credential
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/spec/surface/mcp.md
raw IP URL (30 URLs)
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/src/cli/health/catalog.rs
39 distinct host(s)
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/src/entities/discover.rs
raw IP URL (21 URLs)
Possible obfuscationmediumgenomoncology-biomcp-ba4d160/src/entities/disease/fixtures/medlineplus/chronic_venous_insufficiency_topics.json
very long lines
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/src/render/markdown/evidence.rs
22 distinct host(s)
External endpoints declaredlowgenomoncology-biomcp-ba4d160/src/render/markdown/evidence/tests.rs
10 distinct host(s)
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/src/sources/figshare/tests/construction.rs
raw IP URL (14 URLs)
Internal host / private infrastructure referencemediumgenomoncology-biomcp-ba4d160/src/sources/figshare/tests/construction.rs
shipped content references a private IP range or internal-only host
Egress to a private/loopback hosthighgenomoncology-biomcp-ba4d160/src/sources/figshare/tests/construction.rs
127.0.0.1, 10.0.0.5, 169.254.169.254
Suspicious network referenceslowgenomoncology-biomcp-ba4d160/testdata/sources/myvariant/get_braf_v600e.json
URL shortener (30 URLs)
Suspicious network referenceslowgenomoncology-biomcp-ba4d160/testdata/sources/myvariant/search_braf.json
URL shortener (5 URLs)
Suspicious code patternsmediumgenomoncology-biomcp-ba4d160/tests/test_cbioportal_study_download_timeout_contract.py
dynamic code execution
Suspicious code patternsmediumgenomoncology-biomcp-ba4d160/tests/test_directory_submission_contract.py
OS command execution; dynamic code execution
Suspicious network referencesmediumgenomoncology-biomcp-ba4d160/tests/test_docs_changelog_refresh.py
raw IP URL (13 URLs)
Suspicious code patternshighgenomoncology-biomcp-ba4d160/tests/test_documentation_consistency_audit_contract.py
pipe-to-shell install; dynamic code execution
External endpoints declaredmediumgenomoncology-biomcp-ba4d160/tests/test_source_pages_docs_contract.py
24 distinct host(s)
Vulnerable dependenciesmedium
13 known vulnerabilities in: bincode@1.3.3, fxhash@0.2.1, instant@0.1.13, memmap2@0.5.10, quinn-proto@0.11.14, rustls-pemfile@2.2.0, ttf-parser@0.24.1, anyhow@1.0.102
✔ verified source · pinned genomoncology-biomcp-ba4d160
Check against a policy

The same gate an agent runs before installing (POST /api/v1/trust/biomcp-server/check). Click a policy:

OWASP AI control mapping
5passed
10flagged
0runtime-enforced
5governance

Evaluated against the OWASP Top 10 for LLM Applications (2025) and the OWASP Machine Learning Security Top 10. Expand any control to see the findings.

OWASP Top 10 for LLM Applications
⚠LLM01Prompt Injectionhigh
Adversarial instructions embedded in an artifact that hijack a downstream LLM.
•Prompt-injection phrasing — instruction-subversion language detected (CWE-77)
⚠LLM02Sensitive Information Disclosurehigh
Secrets, credentials or PII shipped inside the artifact.
•Embedded credentials — found: credentials in URL (CWE-798)
•Embedded credentials — found: hardcoded credential (CWE-798)
⚠LLM03Supply Chainmedium
Vulnerable/compromised dependencies, models or archives in the artifact.
•Vulnerable dependencies — 13 known vulnerabilities in: bincode@1.3.3, fxhash@0.2.1, instant@0.1.13, memmap2@0.5.10, quinn-proto@0.11.14, rustls-pemfile@2.2.0, ttf-parser@0.24.1, anyhow@1.0.102 (CWE-1395)
✓LLM04Data and Model PoisoningPassed
Backdoors/poisoning in training data or serialized models.
Behavioral poisoning needs model execution; static check covers unsafe serialization + dataset skew only.
⚠LLM05Improper Output Handlinghigh
Code that pipes model/user output into shell, eval, SQL or paths unsafely.
•Suspicious code patterns — destructive rm -rf / (CWE-78)
•Suspicious code patterns — pipe-to-shell install (CWE-494)
•Suspicious code patterns — OS command execution (CWE-78)
•Path traversal sequences — '../' present in content or name (CWE-22)
•Suspicious code patterns — dynamic code execution (CWE-95)
•Suspicious code patterns — OS command execution; dynamic code execution (CWE-78)
•Suspicious code patterns — pipe-to-shell install; dynamic code execution (CWE-494)
⚠LLM06Excessive Agencyhigh
Over-broad tool/permission surface or unrestricted egress.
•External endpoints declared — 3 distinct host(s)
•Broad capability surface — 3 high-impact capability categories referenced — verify least-privilege (CWE-272)
•External endpoints declared — 1 distinct host(s)
•External endpoints declared — 2 distinct host(s)
•Egress to a private/loopback host — 127.0.0.1 (CWE-918)
•External endpoints declared — 4 distinct host(s)
•External endpoints declared — 12 distinct host(s)
•Broad capability surface — 4 high-impact capability categories referenced — verify least-privilege (CWE-272)
•External endpoints declared — 9 distinct host(s)
•External endpoints declared — 6 distinct host(s)
•External endpoints declared — 7 distinct host(s)
•External endpoints declared — 15 distinct host(s)
•External endpoints declared — 5 distinct host(s)
•External endpoints declared — 8 distinct host(s)
•External endpoints declared — 47 distinct host(s)
•External endpoints declared — 56 distinct host(s)
•External endpoints declared — 48 distinct host(s)
•External endpoints declared — 16 distinct host(s)
•External endpoints declared — 14 distinct host(s)
•External endpoints declared — 39 distinct host(s)
•External endpoints declared — 22 distinct host(s)
•External endpoints declared — 10 distinct host(s)
•Egress to a private/loopback host — 127.0.0.1, 10.0.0.5, 169.254.169.254 (CWE-918)
•External endpoints declared — 24 distinct host(s)
⚠LLM07System Prompt Leakagehigh
Secrets, internal hosts or proprietary logic exposed in shipped prompts.
•Embedded credentials — found: credentials in URL (CWE-798)
•Embedded credentials — found: hardcoded credential (CWE-798)
•Internal host / private infrastructure reference — shipped content references a private IP range or internal-only host (CWE-200)
✓LLM08Vector and Embedding WeaknessesPassed
PII or plaintext source leakage in embedding/vector exports.
Embedding inversion/poisoning is largely runtime; static check covers PII in vector exports.
§LLM09MisinformationGovernance
Artifacts designed to produce false/deceptive output.
Detectable only by runtime behavioral evaluation; addressed via responsible-use attestation.
⚠LLM10Unbounded Consumptionmedium
Unbounded loops/recursion causing DoS or runaway cost.
Enforced at runtime by the gateway (rate limits + spend caps + size caps); static check flags unbounded loops.
•Potentially unbounded loop — an infinite loop (while True / while(1) / for(;;)) may cause runaway consumption (CWE-835)
OWASP Machine Learning Security Top 10
§ML01Input Manipulation (Adversarial)Governance
Models vulnerable to adversarial perturbations.
Requires runtime robustness evaluation; addressed via publisher robustness attestation.
⚠ML02Data Poisoninghigh
Poisoned training datasets with triggers or anomalous distributions.
Static check covers trigger phrasing, PII and label skew; full poisoning detection is runtime.
•Prompt-injection phrasing — instruction-subversion language detected (CWE-77)
§ML03Model InversionGovernance
Training data reconstructable from a model's outputs.
Runtime/evaluation property; addressed via model-card data-provenance + DP attestation.
§ML04Membership InferenceGovernance
Determining whether a record was in the training set.
Runtime/evaluation property; addressed via overfitting disclosure + DP attestation.
✓ML05Model TheftPassed
Unlicensed re-distribution / license-incompatible derivatives.
Static check verifies license declaration; extraction throttling is runtime.
⚠ML06AI Supply Chainmedium
Compromised PyPI/npm packages, typosquats, unsafe serialized models.
•Vulnerable dependencies — 13 known vulnerabilities in: bincode@1.3.3, fxhash@0.2.1, instant@0.1.13, memmap2@0.5.10, quinn-proto@0.11.14, rustls-pemfile@2.2.0, ttf-parser@0.24.1, anyhow@1.0.102 (CWE-1395)
✓ML07Transfer Learning AttackPassed
Backdoored base models / LoRA adapters propagating to derivatives.
Backdoor detection needs behavioral probing; static check covers unsafe serialization + provenance.
§ML08Model SkewingGovernance
Models trained on skewed data producing biased output.
Requires fairness evaluation; addressed via model-card bias/limitations disclosure.
⚠ML09Output Integrityhigh
Middleware tampering with model outputs in transit.
Gateway enforces TLS + response integrity; static check flags output-rewriting code.
•Suspicious code patterns — destructive rm -rf / (CWE-78)
•Suspicious code patterns — pipe-to-shell install (CWE-494)
•Suspicious code patterns — OS command execution (CWE-78)
•Path traversal sequences — '../' present in content or name (CWE-22)
•Suspicious code patterns — dynamic code execution (CWE-95)
•Suspicious code patterns — OS command execution; dynamic code execution (CWE-78)
•Suspicious code patterns — pipe-to-shell install; dynamic code execution (CWE-494)
✓ML10Model Poisoning (Weights)Passed
Tampered model weight files; integrity must be verifiable.
Static check enforces safe formats + records a content hash for downstream verification.

Consume BioMCP programmatically. Authenticate with an API key or session — see Authorize an agent.

# Agents: CHECK BEFORE YOU INSTALL (no auth) — score, grade, level, capability manifest
curl https://ai-supply.store/api/v1/trust/biomcp-server

# Gate against your org policy (returns { pass, violations })
curl -X POST https://ai-supply.store/api/v1/trust/biomcp-server/check \
  -H "Content-Type: application/json" \
  -d '{"minGrade":"B","denyPermissions":["shell"],"denyUnknownEgress":true}'

# CLI
npx ai-supply add biomcp-server

# REST (install → download)
curl -X POST https://ai-supply.store/api/v1/listings/biomcp-server/install \
  -H "Authorization: Bearer $AIM_KEY"

# MCP tool
install_listing({ "slug": "biomcp-server" })
OpenAPI spec →
vlatest
✓ Security: Safe · 1002h ago

Curated mirror — latest upstream source. See the repository for tagged releases.

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