Serveur MCP
BioCosm
io.github.nhoverte/biocosm
Ce que fait ce MCP
Provides biotech intelligence on drugs, diagnostics, targets, companies, clinical phases, clinical outcomes, and probability-of-success estimates.
Capacités
Outils
13
outils
find_by_phase
List drugs/diagnostics at a specific clinical phase.
Schéma d’entrée
{'type': 'object', 'required': ['phase'], 'properties': {'limit': {'type': 'integer', 'default': 100, 'description': 'Maximum results (default 100, max 500)'}, 'phase': {'type': 'string', 'description': 'One of "approved", "on_market", "phase3", "phase2", "phase1",\n "in_development", "cleared", "ldt", "ruo"'}, 'node_type': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'default': None, 'description': 'Optional filter â\x80\x94 "drug", "pipeline", "diagnostic", "target"'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'type': 'array', 'items': {'type': 'object', 'additionalProperties': True}}}, 'x-fastmcp-wrap-result': True}
find_by_target
Find all drugs that target a specific gene/protein.
Schéma d’entrée
{'type': 'object', 'required': ['target_gene'], 'properties': {'limit': {'type': 'integer', 'default': 50, 'description': 'Maximum results (default 50, max 200)'}, 'target_gene': {'type': 'string', 'description': 'Gene symbol or target name (e.g. "EGFR", "KRAS", "PD-1")'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'type': 'array', 'items': {'type': 'object', 'additionalProperties': True}}}, 'x-fastmcp-wrap-result': True}
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
Schéma d’entrée
{'type': 'object', 'required': ['node_id'], 'properties': {'limit': {'type': 'integer', 'default': 30, 'description': 'Maximum results per link type (default 30)'}, 'node_id': {'type': 'string', 'description': 'Source node identifier'}, 'link_type': {'anyOf': [{'type': 'string'}, {'type': 'null'}], 'default': None, 'description': 'Optional filter â\x80\x94 one of "drug_target", "same_target_class",\n "same_company". If None, returns all three groups.'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'anyOf': [{'type': 'object', 'additionalProperties': True}, {'type': 'null'}]}}, 'x-fastmcp-wrap-result': True}
get_company_portfolio
Get a company's full drug/diagnostic portfolio from BioCosm.
Schéma d’entrée
{'type': 'object', 'required': ['company_name'], 'properties': {'company_name': {'type': 'string', 'description': 'Company name (e.g. "Merck", "Roche", "Illumina")'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'anyOf': [{'type': 'object', 'additionalProperties': True}, {'type': 'null'}]}}, 'x-fastmcp-wrap-result': True}
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.
Schéma d’entrée
{'type': 'object', 'properties': {}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'additionalProperties': True}
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.
Schéma d’entrée
{'type': 'object', 'required': ['node_id'], 'properties': {'node_id': {'type': 'string', 'description': 'The node identifier (e.g. "pembrolizumab", "trastuzumab")'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'anyOf': [{'type': 'object', 'additionalProperties': True}, {'type': 'null'}]}}, 'x-fastmcp-wrap-result': True}
get_node_freshness
Get freshness details for a single node: writeup age, enrichment hash match,
staleness score, validation score.
Schéma d’entrée
{'type': 'object', 'required': ['node_id'], 'properties': {'node_id': {'type': 'string', 'description': 'The node identifier (e.g. "pembrolizumab")'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'anyOf': [{'type': 'object', 'additionalProperties': True}, {'type': 'null'}]}}, 'x-fastmcp-wrap-result': True}
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).
Schéma d’entrée
{'type': 'object', 'required': ['node_id'], 'properties': {'node_id': {'type': 'string', 'description': 'Node identifier'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'anyOf': [{'type': 'object', 'additionalProperties': True}, {'type': 'null'}]}}, 'x-fastmcp-wrap-result': True}
get_staleness_report
Get writeup staleness report: overall stats, top stale nodes, data source freshness.
Schéma d’entrée
{'type': 'object', 'properties': {'limit': {'type': 'integer', 'default': 20, 'description': 'Number of top stale nodes to return (default 20)'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'additionalProperties': True}
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.
Schéma d’entrée
{'type': 'object', 'properties': {}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'additionalProperties': True}
get_writeup
Get the full writeup for a BioCosm node, including all sections, citations,
structured data, and validation score.
Schéma d’entrée
{'type': 'object', 'required': ['node_id'], 'properties': {'node_id': {'type': 'string', 'description': 'The node identifier (e.g. "pembrolizumab")'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'anyOf': [{'type': 'object', 'additionalProperties': True}, {'type': 'null'}]}}, 'x-fastmcp-wrap-result': True}
list_by_therapeutic_area
List all nodes in a given therapeutic area.
Schéma d’entrée
{'type': 'object', 'required': ['area'], 'properties': {'area': {'type': 'string', 'description': 'Therapeutic area to search (e.g. "breast cancer", "non-small cell lung cancer")'}, 'limit': {'type': 'integer', 'default': 50, 'description': 'Maximum results (default 50)'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'type': 'array', 'items': {'type': 'object', 'additionalProperties': True}}}, 'x-fastmcp-wrap-result': True}
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.
Schéma d’entrée
{'type': 'object', 'required': ['query'], 'properties': {'limit': {'type': 'integer', 'default': 20, 'description': 'Maximum results to return (default 20, max 100)'}, 'query': {'type': 'string', 'description': 'Search term (e.g. "breast cancer", "pembrolizumab", "Merck")'}}, 'additionalProperties': False}
Schéma de sortie
{'type': 'object', 'required': ['result'], 'properties': {'result': {'type': 'array', 'items': {'type': 'object', 'additionalProperties': True}}}, 'x-fastmcp-wrap-result': True}
Historique
Modifications récentes des outils
Ajouté
get_coverage
17 September 2026 12:45
Ajouté
get_pos_score
17 September 2026 12:45
Ajouté
find_related
17 September 2026 12:45
Ajouté
find_by_phase
17 September 2026 12:45
Ajouté
find_by_target
17 September 2026 12:45
Ajouté
get_node_freshness
17 September 2026 12:45
Ajouté
get_staleness_report
17 September 2026 12:45
Ajouté
get_stats
17 September 2026 12:45
Ajouté
get_company_portfolio
17 September 2026 12:45
Ajouté
list_by_therapeutic_area
17 September 2026 12:45
Ajouté
get_writeup
17 September 2026 12:45
Ajouté
get_node
17 September 2026 12:45
Ajouté
search_nodes
17 September 2026 12:45
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