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BioCosm

by io.github.nhoverte
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Server Details

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

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Status
Healthy
Uptime
100.0% over the last 24 hours
Last Tested
Transport
Streamable HTTP · MCP 2025-11-25
URL
ChatGPT
–
Claude
–

TDQS

A3.9/5.0

Scored across 13 tools

Disambiguation4/5

Tools have mostly distinct purposes, though get_node and get_pos_score both provide probability-of-success data (get_node includes a summary, get_pos_score gives detailed factors). Descriptions clarify the difference, so confusion is minimal.

Naming Consistency4/5

Naming follows a verb_noun pattern but mixes verbs: 'find', 'get', 'list', 'search'. Within the 'get' group, all are consistent. The mix is not chaotic and remains predictable.

Tool Count5/5

13 tools cover the biomedical domain well without being excessive. Each tool has a clear purpose, from searching and listing to fetching detailed node data, statistics, and specialized reports.

Completeness5/5

For a read-only database, the tool set is complete. It supports search, filtered queries, detailed node retrieval, specialized data (PoS, freshness, staleness), and statistics. No obvious gaps for typical query needs.

Available Tools

13 tools
find_by_phaseAInspect

List drugs/diagnostics at a specific clinical phase.

Inputs: phase (required), limit, node_type. Returns: result

find_by_targetBInspect

Find all drugs that target a specific gene/protein.

Inputs: target_gene (required), limit. Returns: result

find_relatedAInspect

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

Inputs: node_id (required), limit, link_type. Returns: result

get_company_portfolioBInspect

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

Inputs: company_name (required). Returns: result

get_coverageAInspect

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.

Inputs: no named parameters. Returns: object

get_nodeAInspect

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.

Inputs: node_id (required). Returns: result

get_node_freshnessAInspect

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

Inputs: node_id (required). Returns: result

get_pos_scoreAInspect

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).

Inputs: node_id (required). Returns: result

get_staleness_reportAInspect

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

Inputs: limit. Returns: object

get_statsAInspect

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

Inputs: no named parameters. Returns: object

get_writeupAInspect

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

Inputs: node_id (required). Returns: result

list_by_therapeutic_areaBInspect

List all nodes in a given therapeutic area.

Inputs: area (required), limit. Returns: result

search_nodesAInspect

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.

Inputs: query (required), limit. Returns: result

Tool Schema Changelog

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