{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_2jwhqn4cr64v","handle":"biomarker-mcp","url":"https://wellknown.network/agents/biomarker-mcp","links":{"self":"https://wellknown.network/agents/biomarker-mcp/record.json","html":"https://wellknown.network/agents/biomarker-mcp","markdown":"https://wellknown.network/agents/biomarker-mcp/record.md","api":"https://wellknown.network/api/v1/agents/biomarker-mcp","status":"https://wellknown.network/api/v1/agents/biomarker-mcp/status","claim":"https://wellknown.network/agents/biomarker-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/biomarker-mcp/claim.json","badge":"https://wellknown.network/agents/biomarker-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/biomarker-mcp/history","tools":"https://wellknown.network/api/v1/agents/biomarker-mcp/tools"},"ard":{"identifier":"urn:air::server:biomarker-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"biomarker-mcp","summary":"Natural language interface for celltype marker query through MCP.","description":"# biomarker-MCP\n\nNatural language interface for celltype marker query through MCP.\n\n## 🪩 What can it do?\n\n- query celltype marker from CellMarker database by natural language\n- will add more database\n\n## ❓ Who is this for?\n\n- Anyone who wants to do query celltype marker with natural language!\n- Agent developers who want to query cell markers for their applications\n\n## 🌐 Where to use it?\n\nYou can use biomarker-mcp in most AI clients, plugins, or agent frameworks that support the MCP:\n\n- AI clients, like Cherry Studio\n- Plugins, like Cline\n- Agent frameworks, like Agno \n\n## 🎬 Demo\n\nA demo showing query celltype markers in a AI client Cherry Studio using natural language based on biomarker-mcp\n\nhttps://github.com/user-attachments/assets/71268f6f-c74d-4142-ad7a-893b411d748a\n\n## 📚 Documentation\n\nscmcphub's complete documentation is available at https://docs.scmcphub.org\n\n## 🏎️ Quickstart\n\n### Install\n\nInstall from PyPI\n```\npip install biomarker-mcp\n```\nyou can test it by running\n```\nbiomarker-mcp run\n```\n\n#### run biomarker-mcp locally\nRefer to the following configuration in your MCP client:\n\ncheck path\n```\n$ which biomarker \n/home/test/bin/biomarker-mcp\n```\n\n```\n\"mcpServers\": {\n  \"biomarker-mcp\": {\n    \"command\": \"/home/test/bin/biomarker-mcp\",\n    \"args\": [\n      \"run\"\n    ]\n  }\n}\n```\n\n#### run biomarker-server remotely\nRefer to the following configuration in your MCP client:\n\nrun it in your server\n```\nbiomarker-mcp run --transport shttp --port 8000\n```\n\nThen configure your MCP client in local AI client, like this:\n```\n\n\"mcpServers\": {\n  \"biomarker-mcp\": {\n    \"url\": \"http://localhost:8000/mcp\"\n  }\n}\n```\n\n## 🤝 Contributing\n\nIf you have any questions, welcome to submit an issue, or contact me(hsh-me@outlook.com). Contributions to the code are also welcome!\n\n## Citing\n\nIf you use biomarker-mcp in for your research, please consider citing  following work: \n> Congxue Hu, Tengyue Li, Yingqi Xu, Xinxin Zhang, Feng Li, Jing Bai, Jing Chen, Wenqi Jiang, Kaiyue Yang, Qi …","publisher":null,"homepage":"https://github.com/scmcphub/biomarker-mcp","repository":"https://github.com/scmcphub/biomarker-mcp","version":"0.2.1","license":null,"protocols":["mcp"],"tags":["ai","agent","bioinformatics","biomarker","celltype","gene","marker","llm","mcp","model","context","protocol","scrna-seq","single","cell"],"pricing":null,"endpoints":[{"url":"pypi:biomarker-mcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","repoUrl":"pypi","summary":"pypi","version":"pypi","description":"pypi","homepageUrl":"pypi"}},"derived":{"capabilities":[{"slug":"data.database","name":"Databases","confidence":0.791,"provenance":"derived"}],"categories":["data"],"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":"biomarker-mcp","registry":"pypi","observedAt":"2026-11-09T00:27:19.395Z","publishedAt":"2025-08-20T17:45:00.518406Z","latestVersion":"0.2.1"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"biomarker-mcp","url":"https://pypi.org/project/biomarker-mcp/","firstSeenAt":"2026-09-09T10:27:11.362Z","fetchedAt":"2026-11-09T00:26:07.186Z","normalizedAt":"2026-11-09T00:26:07.186Z"}]},"firstSeenAt":"2026-09-09T10:27:11.362Z","updatedAt":"2026-11-09T00:27:19.395Z"}