{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_cz8dzkftbe5k","handle":"mcp-ubergraph-query","url":"https://wellknown.network/agents/mcp-ubergraph-query","links":{"self":"https://wellknown.network/agents/mcp-ubergraph-query/record.json","html":"https://wellknown.network/agents/mcp-ubergraph-query","markdown":"https://wellknown.network/agents/mcp-ubergraph-query/record.md","api":"https://wellknown.network/api/v1/agents/mcp-ubergraph-query","status":"https://wellknown.network/api/v1/agents/mcp-ubergraph-query/status","claim":"https://wellknown.network/agents/mcp-ubergraph-query/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/mcp-ubergraph-query/claim.json","badge":"https://wellknown.network/agents/mcp-ubergraph-query/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/mcp-ubergraph-query/history","tools":"https://wellknown.network/api/v1/agents/mcp-ubergraph-query/tools"},"ard":{"identifier":"urn:air::server:mcp-ubergraph-query","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"mcp-ubergraph-query","summary":"MCP server for querying the Ubergraph biomedical ontology SPARQL endpoint","description":"# mcp-ubergraph-query\n\nAn [MCP](https://modelcontextprotocol.io) server for querying the\n[Ubergraph](https://github.com/INCATools/ubergraph) biomedical ontology SPARQL endpoint.\n\nUbergraph is a merged knowledge graph of OBO ontologies including MONDO, UBERON, HP, CHEBI,\nGO, CL, and more. This server exposes four tools that let AI assistants query it naturally.\n\n## Tools\n\n| Tool | Description |\n|---|---|\n| `query_ubergraph` | Execute custom SPARQL SELECT queries |\n| `get_term_info` | Get label, definition, synonyms, and types for an ontology term |\n| `search_terms` | Search terms by label or synonym across ontologies |\n| `get_hierarchy` | Traverse parents, children, ancestors, or descendants |\n\n## Quick Start\n\n### Prerequisites\n\n- Python 3.10+\n- [uv](https://docs.astral.sh/uv/)\n\n### Install\n\n```bash\ngit clone https://github.com/twhetzel/mcp-ubergraph-query\ncd mcp-ubergraph-query\nuv sync --all-extras\n```\n\n### Run the server locally\n\nThe server uses **stdio** (stdin/stdout) for MCP transport. Start it with:\n\n```bash\nuv run mcp-ubergraph-query\n```\n\nOr:\n\n```bash\nuv run python -m ubergraph_query.server\n```\n\nLeave this process running; MCP clients (e.g. Claude Desktop, Cursor) connect by spawning this command and talking over stdin/stdout.\n\n### Configure Claude Desktop\n\nAdd to `~/Library/Application Support/Claude/claude_desktop_config.json`:\n\n```json\n{\n  \"mcpServers\": {\n    \"ubergraph\": {\n      \"command\": \"uv\",\n      \"args\": [\n        \"--directory\",\n        \"/path/to/mcp-ubergraph-query\",\n        \"run\",\n        \"mcp-ubergraph-query\"\n      ]\n    }\n  }\n}\n```\n\n## Configuration\n\nCopy `.env.example` to `.env` and adjust as needed:\n\n```bash\ncp .env.example .env\n```\n\n| Variable | Default | Description |\n|---|---|---|\n| `UBERGRAPH_ENDPOINT` | `https://ubergraph.apps.renci.org/sparql` | SPARQL endpoint URL |\n| `QUERY_TIMEOUT_DEFAULT` | `30` | Default query timeout (seconds) |\n| `QUERY_LIMIT_MAX` | `1000` | Maximum allowed LIMIT value |\n| `ENABLE_QUERY_CACHE` | `true` | Enable in-…","publisher":null,"homepage":"https://github.com/twhetzel/mcp-ubergraph-query#readme","repository":"https://github.com/twhetzel/mcp-ubergraph-query#readme","version":"0.1.0","license":"MIT","protocols":["mcp"],"tags":["bioinformatics","mcp","ontology","sparql","ubergraph"],"pricing":null,"endpoints":[{"url":"pypi:mcp-ubergraph-query","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"}},"derived":{"capabilities":[{"slug":"data.database","name":"Databases","confidence":1,"provenance":"derived"},{"slug":"knowledge.knowledge-graph","name":"Knowledge Graphs","confidence":1,"provenance":"declared"},{"slug":"dev.version-control","name":"Version Control","confidence":0.745,"provenance":"derived"}],"categories":["data","dev","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":"mcp-ubergraph-query","registry":"pypi","observedAt":"2026-10-28T14:24:50.959Z","publishedAt":"2026-02-24T20:48:32.866392Z","latestVersion":"0.1.0"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"mcp-ubergraph-query","url":"https://pypi.org/project/mcp-ubergraph-query/","firstSeenAt":"2026-09-10T05:21:36.018Z","fetchedAt":"2026-10-28T14:24:16.975Z","normalizedAt":"2026-10-28T14:24:16.975Z"}]},"firstSeenAt":"2026-09-10T05:21:36.018Z","updatedAt":"2026-10-28T14:24:50.959Z"}