io.github.nhoverte/biocosm

Tools

• find_by_phase

  List drugs/diagnostics at a specific clinical phase.

  shallow
• find_by_target

  Find all drugs that target a specific gene/protein.

  shallow
• 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

  shallow
• get_company_portfolio

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

  shallow
• 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.

  shallow
• 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.

  shallow
• get_node_freshness

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

  shallow
• 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).

  shallow
• get_staleness_report

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

  shallow
• 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.

  shallow
• get_writeup

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

  shallow
• list_by_therapeutic_area

  List all nodes in a given therapeutic area.

  shallow
• 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.

  shallow

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