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biomcp MCP Server Security Report

genomoncology/biomcp

BioMCP: Biomedical Model Context Protocol

Security Trust Score
Grade A · Strong posture
Tier 1 · Public sourceHigh confidence · 85%latest vmain@561d3fe Repository
Declared MCP capabilities
ToolsResourcesPrompts

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Host genomoncology/biomcp in a governed environment — SSO in front, every tool call attributed and audited.

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The short answer

Is biomcp safe to use?
biomcp scores 90/100 (grade A) on the Canopii Trust Index — strong posture. It passes 14 of the 20 security controls that apply to it, with no confirmed security failures.
How reliable is the security score for biomcp?
We could evaluate 85% of the controls that apply to biomcp. Scores are deterministic — the same source always produces the same score — and a partially-scannable server cannot present a high one, because confidence caps the result. The scanner is open source, so this score can be reproduced independently.
How was biomcp scored?
Its published source was scanned against a fixed catalog of weighted security controls covering code safety, committed secrets, dependency vulnerabilities, tool-description integrity, authentication and transport, and maintenance. A confirmed flaw caps the score outright regardless of what else passes. The full rubric is published.
Reputation674stars119forks1open issues2d agolast commit2yage

Security controlslatest scored version vmain@561d3fe

Each control is evaluated deterministically with evidence. The score is earned from passing controls; a failed guard caps it.

Model–MCP Runtime Guardrails

  • Pass
    Strict JSON Schema EnforcementadditionalProperties:false present

    Tool inputs are constrained (additionalProperties:false), so unexpected arguments can't be smuggled in.

  • Not checked
    Indirect Prompt Injection (IPI) Defensesguardno tools extracted

    Tool/prompt/resource text is free of hidden instructions that could hijack the agent.

  • Not checked
    User-in-the-Loop / Approval Scopeguardno tools extracted

    No over-broad or destructive tools (arbitrary shell, bulk-delete) that warrant human approval.

  • N/A
    Tool Definition Integrityguardno prior version to diff

    Every consecutive version pair is diffed for new injection markers or destructive scope — a risky diff anywhere in history is a rug-pull (fail, durable); benign description drift warns.

Application Security Checks

  • Warn
    No SSRF sinksguard18 occurrences

    Fetching tool-supplied URLs can pivot into internal networks and metadata services.

    architecture/experiments/24-diagnostic-entity-landscape/scripts/diagnostic_landscape/io.py:55architecture/experiments/24-diagnostic-entity-landscape/scripts/diagnostic_landscape/io.py:100architecture/experiments/243-architecture-hpo-phenotype-enrichment-for-clinical-symptoms/scripts/clinical_features_spike/medlineplus.py:79architecture/experiments/243-architecture-hpo-phenotype-enrichment-for-clinical-symptoms/scripts/clinical_summary_medlineplus_probe.py:50

    Fix: Allow-list destinations; reject arbitrary/loopback/link-local URLs.

  • Warn
    No known-vulnerable dependencies17 of 615 runtime deps vulnerable; worst critical

    Runtime dependencies (parsed from the lockfile) are scanned against OSV.dev for published CVEs. Advisory: flagged dependencies lower the score but don't hard-cap it, since transitive reachability is unproven.

    [email protected] — GHSA-qwgh-2vcv-g2f7[email protected] — RUSTSEC-2026-0436[email protected] — RUSTSEC-2024-0384[email protected] — RUSTSEC-2026-0186

    Fix: Upgrade the flagged dependencies past their fixed versions.

  • Warn
    Has a security policyno security policy

    A SECURITY.md gives a private path to report vulnerabilities.

    Fix: Add SECURITY.md with a disclosure contact and process.

  • Pass
    No command-injection sinksguardno sinks found

    Untrusted tool input reaching a shell yields remote code execution.

  • Pass
    No dynamic code executionguardno sinks found

    eval()/exec()/Function() on tool-derived strings allows arbitrary code execution.

  • Pass
    No path traversalguardno sinks found

    Naive path checks let tools read/write outside intended directories (EscapeRoute-class).

  • Pass
    No unsafe deserializationguardno sinks found

    pickle/yaml.load/etc. on untrusted data can execute code.

  • Pass
    No committed secretsguardno secrets found

    Hardcoded keys/tokens in published source are live credentials an attacker can use.

  • Pass
    Credentials sourced from environmentreads credentials from environment

    Reading secrets from env/secret stores avoids hardcoding them.

  • Pass
    Dependencies pinned (lockfile)lockfile present

    A lockfile makes installs reproducible and resistant to silent dependency swaps.

  • Pass
    Actively maintainedrecent commits

    Unmaintained servers don't receive security fixes.

  • Pass
    Repository not archivedguardactive

    Archived repositories will never be patched.

  • Pass
    Declares a licenseMIT

    A clear license is required for legal enterprise use.

  • Pass
    Adoption & popularityestablished adoption

    A small, capped nudge from stars/downloads — widely-used servers get more eyes on bugs. It can never offset a real security failure.

  • Not checked
    Signed releasesnot evaluated

    Signed releases let consumers verify artifacts weren't tampered with.

  • N/A
    No install/post-install scriptsguardno published package

    install hooks run arbitrary code on every consumer at install time.

  • N/A
    Package name not typosquattingguardno published package

    Names mimicking popular packages are a common malware delivery vector.

  • N/A
    Published with provenanceno published package

    Build provenance attests the artifact was built from the claimed source by CI.

  • N/A
    Established maintainerno published package

    Brand-new / single anonymous maintainers raise takeover and malware risk.

Transport & Trust Model

  • Pass
    Execution Sandboxingcontainerized

    A container/sandbox image limits blast radius; a server that runs natively has full host access.

  • Pass
    Network Exposureno bind-all detected

    Binding 0.0.0.0 or exposing debug inspectors widens the attack surface.

  • N/A
    Transport Encryption (TLS)guardno remote endpoints

    Plaintext HTTP exposes traffic and bearer tokens to interception.

  • N/A
    IAM / Authentication Scopingno remote endpoints

    OAuth 2.1 / Protected Resource Metadata gates who can invoke tools.

  • N/A
    Live Endpoint Reachablenot dynamically scanned

    A dynamic scan connected to the declared remote endpoint and it responded — verified live, not a dead URL.

  • N/A
    Authentication Enforced (live)not dynamically scanned

    If the server declares auth is required, it must actually reject anonymous clients. Serving tools to unauthenticated callers is a real exposure.

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Versions

VersionScoreStatus
vmain@561d3felatest90Ascored
vmain@578342190Ascored
vmain@af9b97d90Ascored
vmain@4050fdc90Ascored
vmain@8c420e490Ascored
vmain@0412ebe90Ascored
vmain@175c00490Ascored
vmain@08d721f90Ascored
vmain@631f79090Ascored
vmain@159c68690Ascored
vmain@0b6291490Ascored
vmain@51fef9490Ascored
vmain@7bc323c90Ascored
vmain@73baaff90Ascored
vmain@8e3030a90Ascored
vmain@22459d891Ascored
vmain@d4ab0dc91Ascored
vmain@08ea2cd91Ascored
vmain@8d9daba91Ascored
vmain@a87744391Ascored
vmain@71b1d2f91Ascored
vmain@d6ebb7191Ascored
vmain@90c016991Ascored
vmain@6472b4f91Ascored
vmain@82df3ca90Ascored
vmain@d5bcdd691Ascored
vmain@79573b591Ascored
vmain@a20af5a91Ascored
vmain@45aa9b691Ascored
vmain@8fefcd391Ascored
vmain@14a921891Ascored
vmain@867e2ef91Ascored
vmain@3b1d64591Ascored
vmain@d4867f991Ascored
vmain@25cdfa391Ascored
vmain@65a7a3591Ascored
vmain@1f917bf91Ascored
vmain@d72f50391Ascored
vmain@bb3a1d491Ascored
vmain@cc8c9ec91Ascored
vmain@d57aca591Ascored
vmain@2b3129f91Ascored
vmain@58b9e4a91Ascored
vmain@e95bb7a91Ascored
vmain@19bf49b91Ascored
vmain@27933c991Ascored
vmain@a54331387Bscored
vmain@fb237da87Bscored
vmain@0c8073087Bscored
vmain@86fadf086Bscored
vmain@00ea40b87Bscored
vmain@3d4713987Bscored
vmain@60b39d691Ascored
vmain@89c3cc090Ascored
vmain@5bc386191Ascored
vmain@4ca696390Ascored
vmain@792945991Ascored
vmain@826292690Ascored
vmain@6065a0391Ascored
vmain@1ab70ea91Ascored
vmain@a462cdd91Ascored
vmain@8f3356491Ascored
vmain@903ac2090Ascored
vmain@9247b6b91Ascored
vmain@fb17d7e91Ascored
vmain@edca92991Ascored
vmain@a1c8d0791Ascored
vmain@bf55ce091Ascored
vmain@06d2a1891Ascored

Wondering how this compares? The MCP Security Index tracks grade distribution, committed secrets, and missing authentication across the whole ecosystem, refreshed monthly.