{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_8xd3f6n6yajy","handle":"ncbi-kg-mcp","url":"https://wellknown.network/agents/ncbi-kg-mcp","links":{"self":"https://wellknown.network/agents/ncbi-kg-mcp/record.json","html":"https://wellknown.network/agents/ncbi-kg-mcp","markdown":"https://wellknown.network/agents/ncbi-kg-mcp/record.md","api":"https://wellknown.network/api/v1/agents/ncbi-kg-mcp","status":"https://wellknown.network/api/v1/agents/ncbi-kg-mcp/status","claim":"https://wellknown.network/agents/ncbi-kg-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/ncbi-kg-mcp/claim.json","badge":"https://wellknown.network/agents/ncbi-kg-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json"},"ard":{"identifier":"urn:air::server:ncbi-kg-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"ncbi-kg-mcp","summary":"MCP server for the NCBI Knowledge Graph - query 82K biomedical nodes via any LLM","description":"# ncbi-kg-mcp\n\nMCP server for the [NCBI Knowledge Graph](https://github.com/monideep2255/ncbi_ai_agents) - a BioLink-compliant glucose metabolism graph with 82,517 nodes and 263,404 edges. Query genes, diseases, variants, proteins, pathways, and more from any LLM.\n\n## Install\n\n```bash\npip install ncbi-kg-mcp\n```\n\n## Configure\n\nAdd to your `.mcp.json` (Claude Code, Cursor, Cline, etc.):\n\n```json\n{\n  \"mcpServers\": {\n    \"ncbi-kg\": {\n      \"command\": \"ncbi-kg-mcp\"\n    }\n  }\n}\n```\n\nThat's it. No API keys, no database credentials, no repo cloning needed.\n\n## Tools (5)\n\n| Tool | Input | Description |\n|------|-------|-------------|\n| `query` | `question: str` | Ask a natural language question - auto-translated to Cypher |\n| `cypher` | `query_text: str` | Run a read-only Cypher query directly |\n| `get_stats` | None | Get node and edge counts by type |\n| `get_schema` | None | Get graph schema - node types, relationships, patterns |\n| `get_neighbors` | `node_id: str` | Get 1-hop neighbors of a node (e.g., \"NCBIGene:2645\") |\n\n## Example\n\nAsk your LLM: *\"What genes are associated with MODY?\"*\n\nThe LLM calls the `query` tool, which translates to Cypher, executes against Neo4j, and returns a synthesized answer with raw data.\n\n## Graph Data\n\n- **8 node types**: Gene, Disease, SequenceVariant, BiologicalProcess, MolecularActivity, Protein, CellularComponent, Pathway\n- **15 relationship types**: GENE_ASSOCIATED_WITH_CONDITION, IS_SEQUENCE_VARIANT_OF, CAUSES, INVOLVED_IN, ENABLES, and more\n- **Sources**: NCBI Gene, ClinVar, MedGen, MONDO, GO, UniProt, Reactome\n\n## Configuration\n\n| Env Variable | Default | Description |\n|-------------|---------|-------------|\n| `NCBI_KG_API_URL` | `https://ncbi-kg-api-production.up.railway.app` | API base URL |\n\nOverride the API URL to point to a local backend:\n\n```json\n{\n  \"mcpServers\": {\n    \"ncbi-kg\": {\n      \"command\": \"ncbi-kg-mcp\",\n      \"env\": {\"NCBI_KG_API_URL\": \"http://localhost:8001\"}\n    }\n  }\n}\n```\n\n## Links\n\n- [Full documentation](https:…","publisher":{"name":"Monideep Chakraborti","url":null},"homepage":"https://github.com/monideep2255/ncbi_ai_agents/blob/ncbi-kg/AGENTS_EXTERNAL.md","repository":"https://github.com/monideep2255/ncbi_ai_agents/issues","version":"1.0.1","license":"MIT","protocols":["mcp"],"tags":["mcp"],"pricing":null,"endpoints":[{"url":"pypi:ncbi-kg-mcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","license":"pypi","repoUrl":"pypi","summary":"pypi","version":"pypi","description":"pypi","homepageUrl":"pypi","publisherName":"pypi"}},"derived":{"capabilities":[{"slug":"knowledge.knowledge-graph","name":"Knowledge Graphs","confidence":1,"provenance":"derived"},{"slug":"data.database","name":"Databases","confidence":0.791,"provenance":"derived"}],"categories":["data","knowledge"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"ncbi-kg-mcp","registry":"pypi","observedAt":"2026-09-10T07:21:50.233Z","publishedAt":"2026-03-08T07:41:36.657720Z","latestVersion":"1.0.1"}},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"ncbi-kg-mcp","url":"https://pypi.org/project/ncbi-kg-mcp/","firstSeenAt":"2026-09-10T07:21:12.814Z","fetchedAt":"2026-09-10T07:21:12.814Z","normalizedAt":"2026-09-10T07:21:12.814Z"}]},"firstSeenAt":"2026-09-10T07:21:12.814Z","updatedAt":"2026-09-10T07:21:50.233Z"}