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BioCosm

by nhoverte · remote · no sign-in to list tools · v1.0.0 · published by GitHub user nhoverte

Biotech intelligence for AI agents: drugs, targets, diagnostics, PoS estimates, and writeups.

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13 tools: 13 only read.

Scanned Oct 21, 2026

No check matched anything in the tool definitions. No finding is not a safety guarantee. How the checks work.

claude mcp add --transport http biocosm https://biocosm-mcp.fly.dev/mcp

Tools

Open a tool for its reasons and full description. Descriptions are the publisher's own words, shown as they are.

13 tools

Only reads 13Claude Code: allow
  • find_by_phaseList drugs/diagnostics at a specific clinical phase.No findings

    Why it is in this group

    • The name "find_by_phase" says "find": a word for reading.
    Description, as the server wrote it
    List drugs/diagnostics at a specific clinical phase.
  • find_by_targetFind all drugs that target a specific gene/protein.No findings

    Why it is in this group

    • The name "find_by_target" says "find": a word for reading.
    Description, as the server wrote it
    Find all drugs that target a specific gene/protein.
  • get_company_portfolioGet a company's full drug/diagnostic portfolio from BioCosm.No findings

    Why it is in this group

    • The name "get_company_portfolio" says "get": a word for reading.
    Description, as the server wrote it
    Get a company's full drug/diagnostic portfolio from BioCosm.
  • get_coverageReport BioCosm's actual data coverage so you never mistake missing data for a real-world zero.No findings

    Why it is in this group

    • The name "get_coverage" says "get": a word for reading.
    Description, as the server wrote it
    Report BioCosm's actual data coverage so you never mistake missing data for a real-world zero. An empty or absent field on a node means "not in BioCosm's data," never a true zero. BioCosm is AI-generated and may contain errors.
  • get_nodeGet full details for a single BioCosm node: identity and all name aliases, classification, gene targets and mechanism, therapeutic areas, companies, revenue history where available…No findings

    Why it is in this group

    • The name "get_node" says "get": a word for reading.
    Description, as the server wrote it
    Get full details for a single BioCosm node: identity and all name aliases, classification, gene targets and mechanism, therapeutic areas, companies, revenue history where available (sparse: ~100 drugs, mostly blockbusters, as annualized quarterly estimates; source links when present), probability-of- success predictions for pipeline drugs (with confidence intervals and contributing factors), structured clinical trial outcomes, external cross-references, and writeup availability. Empty fields mean "not in BioCosm's coverage," NOT zero or absent in reality.
  • get_node_freshnessGet freshness details for a single node: writeup age, enrichment hash match, staleness score, validation score.No findings

    Why it is in this group

    • The name "get_node_freshness" says "get": a word for reading.
    Description, as the server wrote it
    Get freshness details for a single node: writeup age, enrichment hash match, staleness score, validation score.
  • get_pos_scoreGet the Probability of Success estimate for a node, including the base rate, adjustment factors with reasoning, confidence interval, and model version.No findings

    Why it is in this group

    • The name "get_pos_score" says "get": a word for reading.
    Description, as the server wrote it
    Get the Probability of Success estimate for a node, including the base rate, adjustment factors with reasoning, confidence interval, and model version. Returns None for nodes without a PoS score (typically only late-stage pipeline drugs are scored).
  • get_staleness_reportGet writeup staleness report: overall stats, top stale nodes, data source freshness.No findings

    Why it is in this group

    • The name "get_staleness_report" says "get": a word for reading.
    Description, as the server wrote it
    Get writeup staleness report: overall stats, top stale nodes, data source freshness.
  • get_statsGet a high-level overview of the BioCosm database: total nodes, writeups, companies, breakdowns by type/status/domain, validation scores, and recent pipeline runs.No findings

    Why it is in this group

    • The name "get_stats" says "get": a word for reading.
    Description, as the server wrote it
    Get a high-level overview of the BioCosm database: total nodes, writeups, companies, breakdowns by type/status/domain, validation scores, and recent pipeline runs.
  • get_writeupGet the full writeup for a BioCosm node, including all sections, citations, structured data, and validation score.No findings

    Why it is in this group

    • The name "get_writeup" says "get": a word for reading.
    Description, as the server wrote it
    Get the full writeup for a BioCosm node, including all sections, citations, structured data, and validation score.
  • list_by_therapeutic_areaList all nodes in a given therapeutic area.No findings

    Why it is in this group

    • The name "list_by_therapeutic_area" says "list": a word for reading.
    Description, as the server wrote it
    List all nodes in a given therapeutic area.
  • search_nodesSearch BioCosm nodes by name, gene symbol, target, therapeutic area, or company.No findings

    Why it is in this group

    • The name "search_nodes" says "search": a word for reading.
    Description, as the server wrote it
    Search BioCosm nodes by name, gene symbol, target, therapeutic area, or company. Results are ranked: exact name/brand matches first, then partial name matches, with a node-type prior (canonical drug/diagnostic nodes rank above gene-target nodes, which rank above ChEMBL salt-form duplicates). Nodes matched only via description/company/area rank last. Each result includes a `name` field for disambiguation.

This is not a safety rating, and no finding is not a safety guarantee. The groups and findings come from fixed checks of the tool definitions the server returned on the date shown, not from its code or what it does when called. How the checks work.

Install

Pinned to version 1.0.0. Values in angle brackets are yours to fill in.

claude mcp add --transport http biocosm https://biocosm-mcp.fly.dev/mcp

Run in a terminal.

Claude Code permissions

Allow the reads, ask before a change, deny the deletes. Paste into .claude/settings.json.

.claude/settings.json
{
  "permissions": {
    "allow": [
      "mcp__biocosm__search_nodes",
      "mcp__biocosm__get_node",
      "mcp__biocosm__get_writeup",
      "mcp__biocosm__list_by_therapeutic_area",
      "mcp__biocosm__get_company_portfolio",
      "mcp__biocosm__get_stats",
      "mcp__biocosm__get_staleness_report",
      "mcp__biocosm__get_node_freshness",
      "mcp__biocosm__find_by_target",
      "mcp__biocosm__find_by_phase",
      "mcp__biocosm__find_related",
      "mcp__biocosm__get_pos_score",
      "mcp__biocosm__get_coverage"
    ],
    "ask": [],
    "deny": []
  }
}

Tools that only read are allowed, tools that change things ask first, tools that delete or cancel are denied. It assumes the server is installed as biocosm. Review it before you use it.