Search / io.github.nhoverte/biocosm
protogridR0· no sign-inBiotech intelligence for AI agents: drugs, targets, diagnostics, PoS estimates, and writeups.
v1.0.0 · active · website · descriptor JSON · versions
{
"mcpServers": {
"biocosm": {
"type": "http",
"url": "https://biocosm-mcp.fly.dev/mcp"
}
}
}claude mcp add --transport http biocosm https://biocosm-mcp.fly.dev/mcp[mcp_servers.biocosm]
url = "https://biocosm-mcp.fly.dev/mcp"
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"biocosm": {
"type": "remote",
"url": "https://biocosm-mcp.fly.dev/mcp",
"enabled": true
}
}
}{
"mcpServers": {
"biocosm": {
"type": "http",
"url": "https://biocosm-mcp.fly.dev/mcp"
}
},
"deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=biocosm&config=eyJ0eXBlIjoiaHR0cCIsInVybCI6Imh0dHBzOi8vYmlvY29zbS1tY3AuZmx5LmRldi9tY3AifQ%3D%3D"
}{
"servers": {
"biocosm": {
"type": "http",
"url": "https://biocosm-mcp.fly.dev/mcp"
}
}
}{
"mcpServers": {
"biocosm": {
"httpUrl": "https://biocosm-mcp.fly.dev/mcp"
}
}
}extensions:
"biocosm":
enabled: true
name: "biocosm"
type: streamable_http
uri: "https://biocosm-mcp.fly.dev/mcp"
timeout: 300
protocol.modernnewest supported version is 2025-11-25; 2026-07-28 not supported, older versions are deprecated until 2027-07-28protocol.statelessonly applies to 2026-07-28 serversprotocol.transportstreamable HTTPprotocol.list_ttlonly applies to 2026-07-28 serversauth.prm, auth.as_metadata, auth.cimdno remote uses OAuthauth.secret_in_urlno templated URLtools.descriptionsevery tool has a descriptiontools.description_lengthdescriptions are concisetools.schemasevery tool has an object input schematools.annotationsno tool declares readOnlyHint or destructiveHint, so clients cannot tell safe calls from risky onestools.directory_hintsno tool declares all four of readOnlyHint, destructiveHint, idempotentHint and openWorldHint; missing: get_writeup (readOnlyHint, destructiveHint, idempotentHint, openWorldHint); find_by_target (readOnlyHint, destructiveHint, idempotentHint, openWorldHint); find_by_phase (readOnlyHint, destructiveHint, idempotentHint, openWorldHint); …tools.token_costabout 1,427 tokens to load every tooltools.api_dumptools are not a one-to-one API dumpstability.changesno tool changes in 30 daysstability.rug_pullno tool changed its meaning under the same namedeps.known_vulns, deps.mcp_sdk_version, deps.resolvableno npm or PyPI packageNo tool definition changes recorded. A server's first observation is its baseline; later probes record what changes.
Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.
+website +reachable +uptime-100% ~updated-124d-ago -no-repository
Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.
| remote | auth | reachable | uptime 30d | p50 | protocol | last ok |
|---|---|---|---|---|---|---|
https://biocosm-mcp.fly.dev/mcp streamable-http | none | yes | 100% | 141 ms | 2025-11-25 | 2026-10-20 |
find_by_phase | List drugs/diagnostics at a specific clinical phase. |
find_by_target | Find all drugs that target a specific gene/protein. |
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 |
get_company_portfolio | Get a company's full drug/diagnostic portfolio from BioCosm. |
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. |
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. |
get_node_freshness | Get freshness details for a single node: writeup age, enrichment hash match, staleness score, validation score. |
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). |
get_staleness_report | Get writeup staleness report: overall stats, top stale nodes, data source freshness. |
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. |
get_writeup | Get the full writeup for a BioCosm node, including all sections, citations, structured data, and validation score. |
list_by_therapeutic_area | List all nodes in a given therapeutic area. |
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. |
Schemas: list_tools.
{
"name": "io.github.nhoverte/biocosm",
"title": "BioCosm",
"$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
"remotes": [
{
"url": "https://biocosm-mcp.fly.dev/mcp",
"type": "streamable-http"
}
],
"version": "1.0.0",
"websiteUrl": "https://biocosm.io/mcp",
"description": "Biotech intelligence for AI agents: drugs, targets, diagnostics, PoS estimates, and writeups."
}