Server definition

Hash: sha256:0b1721e1e32cefe3ae2acd9d04fb9fd902e70ad06bea14b31b2704ee9a3f6186
What it is: What a remote MCP server returned when asked what it offers: 13 tools

The blob, as servednamed by its sha256

{
  "instructions": "Explore thousands of biotech drugs, diagnostics, gene targets, and pipeline compounds. Nodes carry structured metadata; many also have full analytical writeups (summary, mechanism, trial design, probability-of-success estimate, risks, assessment) with citations, and link to targets, companies, revenue, and trial outcomes. Start with search_nodes, then get_node / get_writeup; find_by_phase, find_by_target, and get_company_portfolio handle portfolio queries; get_coverage reports what data is and isn't populated.\n\nIMPORTANT - read before relying on anything: BioCosm is an AI-powered, automatically generated research tool. Despite substantial data-quality engineering (cross-source checks, citation verification, deduplication), individual facts may be incomplete, out of date, or outright wrong. Coverage is uneven - e.g. only ~100 drugs have revenue data, and PoS scores cover pipeline drugs. An empty or missing field means 'not in BioCosm's data,' NEVER a real-world zero. Treat everything as a research starting point, verify against primary sources (ClinicalTrials.gov, FDA, SEC filings), and note this is not investment or medical advice.",
  "tools": [
    {
      "description": "List drugs/diagnostics at a specific clinical phase.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "limit": {
            "default": 100,
            "description": "Maximum results (default 100, max 500)",
            "type": "integer"
          },
          "node_type": {
            "anyOf": [
              {
                "type": "string"
              },
              {
                "type": "null"
              }
            ],
            "default": null,
            "description": "Optional filter — \"drug\", \"pipeline\", \"diagnostic\", \"target\""
          },
          "phase": {
            "description": "One of \"approved\", \"on_market\", \"phase3\", \"phase2\", \"phase1\",\n   \"in_development\", \"cleared\", \"ldt\", \"ruo\"",
            "type": "string"
          }
        },
        "required": [
          "phase"
        ],
        "type": "object"
      },
      "name": "find_by_phase",
      "outputSchema": {
        "properties": {
          "result": {
            "items": {
              "additionalProperties": true,
              "type": "object"
            },
            "type": "array"
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    },
    {
      "description": "Find all drugs that target a specific gene/protein.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "limit": {
            "default": 50,
            "description": "Maximum results (default 50, max 200)",
            "type": "integer"
          },
          "target_gene": {
            "description": "Gene symbol or target name (e.g. \"EGFR\", \"KRAS\", \"PD-1\")",
            "type": "string"
          }
        },
        "required": [
          "target_gene"
        ],
        "type": "object"
      },
      "name": "find_by_target",
      "outputSchema": {
        "properties": {
          "result": {
            "items": {
              "additionalProperties": true,
              "type": "object"
            },
            "type": "array"
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    },
    {
      "description": "Find nodes connected to a given node. Three relationship types are\nderived on-the-fly:\n  - \"drug_target\": for a drug, the targets it hits (and vice versa for a\n                   target node, the drugs that hit it)\n  - \"same_company\": drugs sharing a company with this node\n  - \"same_target_class\": drugs with the same mechanism_class",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "limit": {
            "default": 30,
            "description": "Maximum results per link type (default 30)",
            "type": "integer"
          },
          "link_type": {
            "anyOf": [
              {
                "type": "string"
              },
              {
                "type": "null"
              }
            ],
            "default": null,
            "description": "Optional filter — one of \"drug_target\", \"same_target_class\",\n       \"same_company\". If None, returns all three groups."
          },
          "node_id": {
            "description": "Source node identifier",
            "type": "string"
          }
        },
        "required": [
          "node_id"
        ],
        "type": "object"
      },
      "name": "find_related",
      "outputSchema": {
        "properties": {
          "result": {
            "anyOf": [
              {
                "additionalProperties": true,
                "type": "object"
              },
              {
                "type": "null"
              }
            ]
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    },
    {
      "description": "Get a company's full drug/diagnostic portfolio from BioCosm.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "company_name": {
            "description": "Company name (e.g. \"Merck\", \"Roche\", \"Illumina\")",
            "type": "string"
          }
        },
        "required": [
          "company_name"
        ],
        "type": "object"
      },
      "name": "get_company_portfolio",
      "outputSchema": {
        "properties": {
          "result": {
            "anyOf": [
              {
                "additionalProperties": true,
                "type": "object"
              },
              {
                "type": "null"
              }
            ]
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    },
    {
      "description": "Report BioCosm's actual data coverage so you never mistake missing data for\na real-world zero. An empty or absent field on a node means \"not in BioCosm's\ndata,\" never a true zero. BioCosm is AI-generated and may contain errors.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {},
        "type": "object"
      },
      "name": "get_coverage",
      "outputSchema": {
        "additionalProperties": true,
        "type": "object"
      }
    },
    {
      "description": "Get full details for a single BioCosm node: identity and all name aliases,\nclassification, gene targets and mechanism, therapeutic areas, companies,\nrevenue history where available (sparse: ~100 drugs, mostly blockbusters,\nas annualized quarterly estimates; source links when present), probability-of-\nsuccess predictions for pipeline drugs (with confidence intervals and\ncontributing factors), structured clinical trial outcomes, external\ncross-references, and writeup availability. Empty fields mean \"not in BioCosm's\ncoverage,\" NOT zero or absent in reality.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "node_id": {
            "description": "The node identifier (e.g. \"pembrolizumab\", \"trastuzumab\")",
            "type": "string"
          }
        },
        "required": [
          "node_id"
        ],
        "type": "object"
      },
      "name": "get_node",
      "outputSchema": {
        "properties": {
          "result": {
            "anyOf": [
              {
                "additionalProperties": true,
                "type": "object"
              },
              {
                "type": "null"
              }
            ]
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    },
    {
      "description": "Get freshness details for a single node: writeup age, enrichment hash match,\nstaleness score, validation score.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "node_id": {
            "description": "The node identifier (e.g. \"pembrolizumab\")",
            "type": "string"
          }
        },
        "required": [
          "node_id"
        ],
        "type": "object"
      },
      "name": "get_node_freshness",
      "outputSchema": {
        "properties": {
          "result": {
            "anyOf": [
              {
                "additionalProperties": true,
                "type": "object"
              },
              {
                "type": "null"
              }
            ]
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    },
    {
      "description": "Get the Probability of Success estimate for a node, including the\nbase rate, adjustment factors with reasoning, confidence interval, and\nmodel version.\n\nReturns None for nodes without a PoS score (typically only late-stage\npipeline drugs are scored).",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "node_id": {
            "description": "Node identifier",
            "type": "string"
          }
        },
        "required": [
          "node_id"
        ],
        "type": "object"
      },
      "name": "get_pos_score",
      "outputSchema": {
        "properties": {
          "result": {
            "anyOf": [
              {
                "additionalProperties": true,
                "type": "object"
              },
              {
                "type": "null"
              }
            ]
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    },
    {
      "description": "Get writeup staleness report: overall stats, top stale nodes, data source freshness.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "limit": {
            "default": 20,
            "description": "Number of top stale nodes to return (default 20)",
            "type": "integer"
          }
        },
        "type": "object"
      },
      "name": "get_staleness_report",
      "outputSchema": {
        "additionalProperties": true,
        "type": "object"
      }
    },
    {
      "description": "Get a high-level overview of the BioCosm database: total nodes, writeups,\ncompanies, breakdowns by type/status/domain, validation scores, and recent\npipeline runs.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {},
        "type": "object"
      },
      "name": "get_stats",
      "outputSchema": {
        "additionalProperties": true,
        "type": "object"
      }
    },
    {
      "description": "Get the full writeup for a BioCosm node, including all sections, citations,\nstructured data, and validation score.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "node_id": {
            "description": "The node identifier (e.g. \"pembrolizumab\")",
            "type": "string"
          }
        },
        "required": [
          "node_id"
        ],
        "type": "object"
      },
      "name": "get_writeup",
      "outputSchema": {
        "properties": {
          "result": {
            "anyOf": [
              {
                "additionalProperties": true,
                "type": "object"
              },
              {
                "type": "null"
              }
            ]
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    },
    {
      "description": "List all nodes in a given therapeutic area.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "area": {
            "description": "Therapeutic area to search (e.g. \"breast cancer\", \"non-small cell lung cancer\")",
            "type": "string"
          },
          "limit": {
            "default": 50,
            "description": "Maximum results (default 50)",
            "type": "integer"
          }
        },
        "required": [
          "area"
        ],
        "type": "object"
      },
      "name": "list_by_therapeutic_area",
      "outputSchema": {
        "properties": {
          "result": {
            "items": {
              "additionalProperties": true,
              "type": "object"
            },
            "type": "array"
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    },
    {
      "description": "Search BioCosm nodes by name, gene symbol, target, therapeutic area, or company.\n\nResults are ranked: exact name/brand matches first, then partial name\nmatches, with a node-type prior (canonical drug/diagnostic nodes rank above\ngene-target nodes, which rank above ChEMBL salt-form duplicates). Nodes\nmatched only via description/company/area rank last. Each result includes a\n`name` field for disambiguation.",
      "inputSchema": {
        "additionalProperties": false,
        "properties": {
          "limit": {
            "default": 20,
            "description": "Maximum results to return (default 20, max 100)",
            "type": "integer"
          },
          "query": {
            "description": "Search term (e.g. \"breast cancer\", \"pembrolizumab\", \"Merck\")",
            "type": "string"
          }
        },
        "required": [
          "query"
        ],
        "type": "object"
      },
      "name": "search_nodes",
      "outputSchema": {
        "properties": {
          "result": {
            "items": {
              "additionalProperties": true,
              "type": "object"
            },
            "type": "array"
          }
        },
        "required": [
          "result"
        ],
        "type": "object",
        "x-fastmcp-wrap-result": true
      }
    }
  ]
}

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