BioCosm

Measured conclusion: Deep-tested. L2 outcome: tools_ok.

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

Add to your agent

Copy this into your MCP client config:

{
  "mcpServers": {
    "BioCosm": {
      "url": "https://biocosm-mcp.fly.dev/mcp",
      "transport": "streamable-http"
    }
  }
}

Measured tools (13)

• search_nodes

  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.

  Parameters:

  • query (required) — string — Search term (e.g. "breast cancer", "pembrolizumab", "Merck")
  • limit — integer — Maximum results to return (default 20, max 100)

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• get_node

  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.

  Parameters:

  • node_id (required) — string — The node identifier (e.g. "pembrolizumab", "trastuzumab")

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• get_writeup

  Get the full writeup for a BioCosm node, including all sections, citations, structured data, and validation score.

  Parameters:

  • node_id (required) — string — The node identifier (e.g. "pembrolizumab")

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• list_by_therapeutic_area

  List all nodes in a given therapeutic area.

  Parameters:

  • area (required) — string — Therapeutic area to search (e.g. "breast cancer", "non-small cell lung cancer")
  • limit — integer — Maximum results (default 50)

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• get_company_portfolio

  Get a company's full drug/diagnostic portfolio from BioCosm.

  Parameters:

  • company_name (required) — string — Company name (e.g. "Merck", "Roche", "Illumina")

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• get_stats

  Get a high-level overview of the BioCosm database: total nodes, writeups, companies, breakdowns by type/status/domain, validation scores, and recent pipeline runs.

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• get_staleness_report

  Get writeup staleness report: overall stats, top stale nodes, data source freshness.

  Parameters:

  • limit — integer — Number of top stale nodes to return (default 20)

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• get_node_freshness

  Get freshness details for a single node: writeup age, enrichment hash match, staleness score, validation score.

  Parameters:

  • node_id (required) — string — The node identifier (e.g. "pembrolizumab")

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• find_by_target

  Find all drugs that target a specific gene/protein.

  Parameters:

  • target_gene (required) — string — Gene symbol or target name (e.g. "EGFR", "KRAS", "PD-1")
  • limit — integer — Maximum results (default 50, max 200)

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• find_by_phase

  List drugs/diagnostics at a specific clinical phase.

  Parameters:

  • phase (required) — string — One of "approved", "on_market", "phase3", "phase2", "phase1", "in_development", "cleared", "ldt", "ruo"
  • limit — integer — Maximum results (default 100, max 500)
  • node_type — Optional filter — "drug", "pipeline", "diagnostic", "target"

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• find_related

  Find nodes connected to a given node. Three relationship types are derived on-the-fly: - "drug_target": for a drug, the targets it hits (and vice versa for a target node, the drugs that hit it) - "same_company": drugs sharing a company with this node - "same_target_class": drugs with the same mechanism_class

  Parameters:

  • node_id (required) — string — Source node identifier
  • limit — integer — Maximum results per link type (default 30)
  • link_type — Optional filter — one of "drug_target", "same_target_class", "same_company". If None, returns all three groups.

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• get_pos_score

  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).

  Parameters:

  • node_id (required) — string — Node identifier

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

• get_coverage

  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.

  Hints: read-only not declared · destructive not declared · idempotent not declared · open-world not declared

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