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io.github.unibio-intelligence/biomedmcp

io.github.unibio-intelligence/biomedmcp v0.2.4

Security Trust Score
Grade B · Moderate posture
Tier 1 · Public sourceHigh confidence · 92%
Declared MCP capabilities

Host io.github.unibio-intelligence/biomedmcp in a governed environment — SSO in front, every tool call attributed and audited.

Reputation1stars0forks0open issuestodaylast commit<1yage

Security controls

Deterministic, evidence-backed. Score earned from passing controls; a failed guard caps it.

Model–MCP Runtime Guardrails

  • Pass
    Indirect Prompt Injection (IPI) Defensesguardno injection markers

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

  • Pass
    Strict JSON Schema EnforcementadditionalProperties:false present

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

  • Pass
    User-in-the-Loop / Approval Scopeguardno destructive tool scope

    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 dynamic code executionguard2 occurrences (build/test paths only)

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

    scripts/benchmark-study-algorithms.py:76scripts/benchmark-study-algorithms.py:77

    Fix: Remove eval/exec; parse and dispatch explicitly.

  • Warn
    No known-vulnerable dependencies16 of 86 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-5p39-cfhj-2xmp[email protected] — GHSA-82r6-8w77-94w6[email protected] — PYSEC-2026-4024[email protected] — PYSEC-2026-4025

    Fix: Upgrade the flagged dependencies past their fixed versions.

  • Warn
    Established maintainerrecently published

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

    Fix: Publish under an established account/org; add multiple maintainers.

  • 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.

  • Warn
    Adoption & popularitylimited adoption

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

    Fix: Adoption grows naturally with real-world use; this never gates the score.

  • Pass
    No command-injection sinksguardno sinks found

    Untrusted tool input reaching a shell yields remote code execution.

  • Pass
    No path traversalguardno sinks found

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

  • Pass
    No SSRF sinksguardno sinks found

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

  • 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
    Package name not typosquattingguarddistinct package name

    Names mimicking popular packages are a common malware delivery vector.

  • Pass
    Actively maintainedrecent commits

    Unmaintained servers don't receive security fixes.

  • Pass
    Repository not archivedguardactive

    Archived repositories will never be patched.

  • Pass
    Declares a licenseApache-2.0

    A clear license is required for legal enterprise use.

  • Not checked
    No install/post-install scriptsguardnot determinable from PyPI metadata

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

  • Not checked
    Published with provenancenot determinable

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

  • Not checked
    Signed releasesnot evaluated

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

Transport & Trust Model

  • Warn
    IAM / Authentication Scopingno authentication handling detected

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

    Fix: Implement OAuth 2.1 with a .well-known/oauth-protected-resource document.

  • Warn
    Network Exposurebinds 0.0.0.0

    Binding 0.0.0.0 or exposing debug inspectors widens the attack surface.

    Fix: Bind to 127.0.0.1 by default; never ship open debug endpoints.

  • Pass
    Transport Encryption (TLS)guardall remotes use HTTPS

    Plaintext HTTP exposes traffic and bearer tokens to interception.

  • Pass
    Execution Sandboxingcontainerized

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

  • 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.

Tools (77)

{query}query_qtlget_sampleblast_searchget_metadatasearch_drugssearch_termsannotate_textget_complexessearch_by_ndcbatch_annotatecompare_trialsget_annotationget_tf_targetsquery_proteinssearch_recallssearch_studiessearch_targetsadvanced_searchget_annotationssearch_pathwaysget_drug_detailsget_interactionsget_pathway_infoget_protein_infoquery_expressionsearch_compoundssearch_drug_infoget_antibody_infoget_assay_detailsget_mirna_targetsget_ontology_infoget_sequence_dataget_study_detailssearch_by_filterssearch_cell_linessearch_propertiesget_analytics_dataget_cell_line_infoget_drug_shortagesget_target_detailssearch_drug_labelsget_expression_dataget_ligand_receptorget_pathway_diagramget_protein_classesanalyze_localizationbatch_protein_lookupdownload_genome_dataget_compound_detailsget_cross_referencesget_enzyme_substrateget_ontology_metricsget_trial_statisticsrecommend_ontologiessearch_bioactivitiesbatch_compound_lookupfind_pathways_by_genesearch_adverse_eventsget_recruiting_studiesconvert_gene_to_ensemblget_drug_label_by_setidget_drug_label_sectionsget_gene_effect_profileadvanced_property_searchfind_pathways_by_diseaseget_protein_interactionssearch_device_clearancessearch_gene_dependenciessearch_specialized_trialsanalyze_compound_propertiesanalyze_disease_associationcompare_compound_activitiescompare_expression_profilesfind_selective_dependenciessearch_by_application_numberget_completed_studies_with_results