{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_2zyw6mq6yxzp","handle":"iflow-mcp-pubtator-mcp-server","url":"https://wellknown.network/agents/iflow-mcp-pubtator-mcp-server","links":{"self":"https://wellknown.network/agents/iflow-mcp-pubtator-mcp-server/record.json","html":"https://wellknown.network/agents/iflow-mcp-pubtator-mcp-server","markdown":"https://wellknown.network/agents/iflow-mcp-pubtator-mcp-server/record.md","api":"https://wellknown.network/api/v1/agents/iflow-mcp-pubtator-mcp-server","status":"https://wellknown.network/api/v1/agents/iflow-mcp-pubtator-mcp-server/status","claim":"https://wellknown.network/agents/iflow-mcp-pubtator-mcp-server/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/iflow-mcp-pubtator-mcp-server/claim.json","badge":"https://wellknown.network/agents/iflow-mcp-pubtator-mcp-server/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/iflow-mcp-pubtator-mcp-server/history","tools":"https://wellknown.network/api/v1/agents/iflow-mcp-pubtator-mcp-server/tools"},"ard":{"identifier":"urn:air::server:iflow-mcp-pubtator-mcp-server","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"iflow-mcp_pubtator-mcp-server","summary":"A biomedical literature annotation and relationship mining server based on PubTator3","description":"# PubTator MCP Server\n[![smithery badge](https://smithery.ai/badge/@JackKuo666/pubtator-mcp-server)](https://smithery.ai/server/@JackKuo666/pubtator-mcp-server)\n\n🔍 A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.\n\nPubTator MCP Server provides AI assistants with access to the PubTator3 biomedical literature annotation system through the Model Context Protocol (MCP). It allows AI models to programmatically search scientific literature, obtain annotation information, and analyze entity relationships.\n\n🤝 Contribute • 📝 Report Issues\n\n## ✨ Core Features\n- 🔎 Literature Annotation Export: Support exporting PubTator annotation results in multiple formats ✅\n- 🚀 Entity ID Lookup: Query standard identifiers for biological concepts through free text ✅\n- 📊 Relationship Mining: Discover biomedical relationships between entities ✅\n- 📄 Literature Search: Support literature retrieval by keywords and entity IDs ✅\n- 🧠 Batch Processing: Support batch export of annotation information from search results ✅\n\n## 🚀 Quick Start\n\n### Requirements\n\n- Python 3.10+\n- FastMCP library\n\n### Installation\n\n#### Via Smithery\n\nUse [Smithery](https://smithery.ai/server/@JackKuo666/pubtator-mcp-server) to automatically install PubTator Server:\n\n##### Claude\n\n```sh\nnpx -y @smithery/cli@latest install @JackKuo666/pubtator-mcp-server --client claude --config \"{}\"\n```\n\n##### Cursor\n\nPaste in Settings → Cursor Settings → MCP → Add new server:\n- Mac/Linux  \n```s\nnpx -y @smithery/cli@latest run @JackKuo666/pubtator-mcp-server --client cursor --config \"{}\" \n```\n\n##### Windsurf\n```sh\nnpx -y @smithery/cli@latest install @JackKuo666/pubtator-mcp-server --client windsurf --config \"{}\"\n```\n\n##### CLine\n```sh\nnpx -y @smithery/cli@latest install @JackKuo666/pubtator-mcp-server --client cline --config \"{}\"\n```\n\n#### Manual Installation\n\n1. Clone the repository:\n   ```\n   git clone https://github.com/JackKuo666/PubTator-…","publisher":null,"homepage":"https://github.com/JackKuo666/PubTator-MCP-Server","repository":"https://github.com/JackKuo666/PubTator-MCP-Server","version":"0.1.1","license":"MIT","protocols":["mcp"],"tags":["mcp"],"pricing":null,"endpoints":[{"url":"pypi:iflow-mcp_pubtator-mcp-server","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":"dev.version-control","name":"Version Control","confidence":1,"provenance":"derived"}],"categories":["dev"],"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":"iflow-mcp_pubtator-mcp-server","registry":"pypi","observedAt":"2026-09-15T19:23:33.847Z","publishedAt":"2025-11-14T03:22:18.265010Z","latestVersion":"0.1.1"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"iflow-mcp_pubtator-mcp-server","url":"https://pypi.org/project/iflow-mcp_pubtator-mcp-server/","firstSeenAt":"2026-09-09T20:25:13.827Z","fetchedAt":"2026-09-15T19:22:49.285Z","normalizedAt":"2026-09-15T19:22:49.285Z"}]},"firstSeenAt":"2026-09-09T20:25:13.827Z","updatedAt":"2026-09-15T19:23:33.847Z"}