{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_49zjkhbm36ny","handle":"nmdc-mcp","url":"https://wellknown.network/agents/nmdc-mcp","links":{"self":"https://wellknown.network/agents/nmdc-mcp/record.json","html":"https://wellknown.network/agents/nmdc-mcp","markdown":"https://wellknown.network/agents/nmdc-mcp/record.md","api":"https://wellknown.network/api/v1/agents/nmdc-mcp","status":"https://wellknown.network/api/v1/agents/nmdc-mcp/status","claim":"https://wellknown.network/agents/nmdc-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/nmdc-mcp/claim.json","badge":"https://wellknown.network/agents/nmdc-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/nmdc-mcp/history","tools":"https://wellknown.network/api/v1/agents/nmdc-mcp/tools"},"ard":{"identifier":"urn:air::server:nmdc-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"nmdc-mcp","summary":"FastMCP-based tool for writing prompts against data in the NMDC (National Microbiome Data Collaborative) database","description":"# NMDC MCP\n\nA fastmcp-based tool for writing prompts against data in the NMDC database.\n\n## Installation\n\nYou can install the package from source using uv:\n\n```bash\nuv sync\n```\n\n## Usage\n\nYou can use the CLI:\n\n```bash\nnmdc-mcp\n```\n\nOr import in your Python code: # TODO incorrect instructions\n\n```python\nfrom nmdc_mcp.main import create_mcp\n\nmcp = create_mcp()\nmcp.run()\n```\n\nOr utilize the `nmdc_mcp.client`. This client uses OpenAI API and assumes you have `API_KEY` set in a .env file in the root directory of this repo. The `BASE_URL` and `MODEL` are also customizable in .env. For PNNL staff that want to run via this client - the `BASE_URL` and `MODEL` are specific. Contact Olivia Hess if you need help setting these values up.\n\n```bash\nuv run 'path/to/nmdc_mcp/client.py' 'path/to/nmdc_mcp/main.py'\n```\n\nOr using python\n\n```bash\npython 'path/to/nmdc_mcp/client.py' 'path/to/nmdc_mcp/main.py'\n```\n\n## Development\n\n### Local Setup\n\n```bash\n# Clone the repository\ngit clone https://github.com/microbiomedata/nmdc-mcp.git\ncd nmdc-mcp\n\n# Install development dependencies\nmake dev\n```\n\n### Development Workflow\n\nThe project uses a comprehensive Makefile for development tasks:\n\n```bash\n# Run all development checks (tests, formatting, linting, type checking)\nmake all\n\n# Individual commands\nmake dev           # Install development dependencies\nmake test-coverage # Run tests with coverage\nmake format        # Format code with black\nmake lint          # Lint with ruff\nmake mypy          # Type checking\nmake deptry        # Check for unused dependencies\nmake build         # Build package\n```\n\n### Testing\n\n```bash\n# Run all tests with coverage\nmake test-coverage\n\n# Run specific test types\nmake test-unit         # Unit tests only\nmake test-integration  # Integration tests\nmake test-real-api     # Tests against real NMDC API\nmake test-mcp          # Test MCP protocol\n```\n\n### MCP Integration\n\n#### Claude Desktop Setup\nAdd to `~/Library/Application Support/Claude/claude_desktop_config.json`…","publisher":null,"homepage":"https://github.com/microbiomedata/nmdc-mcp/blob/main/README.md","repository":"https://github.com/microbiomedata/nmdc-mcp/issues","version":"0.6.0","license":"MIT","protocols":["mcp"],"tags":["biosamples","fastmcp","mcp","microbiome","model-context-protocol","nmdc"],"pricing":null,"endpoints":[{"url":"pypi:nmdc-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":"productivity.tasks","name":"Tasks & To-do","confidence":1,"provenance":"derived"},{"slug":"dev.package-management","name":"Packages & Dependencies","confidence":0.859,"provenance":"derived"},{"slug":"code.testing","name":"Testing","confidence":0.825,"provenance":"derived"}],"categories":["code","dev","productivity"],"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":"nmdc-mcp","registry":"pypi","observedAt":"2026-11-09T22:23:28.510Z","publishedAt":"2025-08-12T17:01:17.813590Z","latestVersion":"0.6.0"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"nmdc-mcp","url":"https://pypi.org/project/nmdc-mcp/","firstSeenAt":"2026-09-10T08:25:19.587Z","fetchedAt":"2026-11-09T22:21:41.833Z","normalizedAt":"2026-11-09T22:21:41.833Z"}]},"firstSeenAt":"2026-09-10T08:25:19.587Z","updatedAt":"2026-11-09T22:23:28.510Z"}