{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_w3bry8qcbv9v","handle":"ols-mcp","url":"https://wellknown.network/agents/ols-mcp","links":{"self":"https://wellknown.network/agents/ols-mcp/record.json","html":"https://wellknown.network/agents/ols-mcp","markdown":"https://wellknown.network/agents/ols-mcp/record.md","api":"https://wellknown.network/api/v1/agents/ols-mcp","status":"https://wellknown.network/api/v1/agents/ols-mcp/status","claim":"https://wellknown.network/agents/ols-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/ols-mcp/claim.json","badge":"https://wellknown.network/agents/ols-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/ols-mcp/history","tools":"https://wellknown.network/api/v1/agents/ols-mcp/tools"},"ard":{"identifier":"urn:air::server:ols-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"ols-mcp","summary":"MCP for retrieving things from the Ontology Lookup Service","description":"# ols-mcp\n\nA Model Context Protocol (MCP) server for retrieving information from the Ontology Lookup Service (OLS). \n\nThis package provides tools for searching ontologies, retrieving ontology details, and accessing ontology terms through a standardized MCP interface.\n\n## Installation\n\n### From PyPI\n\n```bash\npip install ols-mcp\n```\n\n### From Source\n\n```bash\n# Clone the repository\ngit clone https://github.com/contextualizer-ai/ols-mcp.git\ncd ols-mcp\n\n# Install with uv (recommended)\nuv sync --group dev\n\n# Or with pip\npip install -e .\n```\n\n## Usage\n\n### As MCP Server\n\nThe primary use case is as an MCP server that provides ontology search capabilities to AI agents and applications.\n\n#### Claude Desktop Integration\n\nAdd to your Claude Desktop configuration (`~/Library/Application Support/Claude/claude_desktop_config.json`):\n\n```json\n{\n  \"mcpServers\": {\n    \"ols-mcp\": {\n      \"command\": \"ols-mcp\",\n      \"args\": []\n    }\n  }\n}\n```\n\n#### Claude Code Integration\n\n```bash\nclaude mcp add ols-mcp\n```\n\n#### Goose Integration\n\n```bash\ngoose session start --with-mcp \"ols-mcp\"\n```\n\n### Available Tools\n\nThe MCP server provides three main tools:\n\n1. **`search_all_ontologies`** - Search across all ontologies in OLS\n2. **`get_ontology_info`** - Get detailed information about a specific ontology\n3. **`get_terms_from_ontology`** - Retrieve terms from a specific ontology\n\n### Direct Python Usage\n\n```python\nfrom ols_mcp.tools import search_all_ontologies, get_ontology_info, get_terms_from_ontology\n\n# Search for biological terms\nresults = search_all_ontologies(\"apoptosis\", max_results=5)\n\n# Get information about Gene Ontology\ngo_info = get_ontology_info(\"go\")\n\n# Get terms from a specific ontology\nterms = get_terms_from_ontology(\"go\", max_results=10)\n```\n\n### CLI Usage\n\n#### Running the MCP Server\n\nRun the MCP server directly:\n\n```bash\nols-mcp\n```\n\n#### Testing Individual Tools\n\nYou can test the tools directly using Python:\n\n```bash\n# Search for biological terms across all ontologies\nuv run …","publisher":null,"homepage":"https://github.com/justaddcoffee/ols-mcp#readme","repository":"https://github.com/justaddcoffee/ols-mcp#readme","version":"0.1.5","license":"MIT License\n        \n        Copyright (c) 2024 Justin Reese\n  …","protocols":["mcp"],"tags":["bioinformatics","mcp","ols","ontology"],"pricing":null,"endpoints":[{"url":"pypi:ols-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"}},"derived":{"capabilities":[{"slug":"dev.version-control","name":"Version Control","confidence":1,"provenance":"derived"},{"slug":"knowledge.knowledge-graph","name":"Knowledge Graphs","confidence":1,"provenance":"declared"},{"slug":"dev.package-management","name":"Packages & Dependencies","confidence":0.768,"provenance":"derived"}],"categories":["dev","knowledge"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; 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