{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_t5qd8j96c48s","handle":"nucleotide-archive-mcp","url":"https://wellknown.network/agents/nucleotide-archive-mcp","links":{"self":"https://wellknown.network/agents/nucleotide-archive-mcp/record.json","html":"https://wellknown.network/agents/nucleotide-archive-mcp","markdown":"https://wellknown.network/agents/nucleotide-archive-mcp/record.md","api":"https://wellknown.network/api/v1/agents/nucleotide-archive-mcp","status":"https://wellknown.network/api/v1/agents/nucleotide-archive-mcp/status","claim":"https://wellknown.network/agents/nucleotide-archive-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/nucleotide-archive-mcp/claim.json","badge":"https://wellknown.network/agents/nucleotide-archive-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/nucleotide-archive-mcp/history","tools":"https://wellknown.network/api/v1/agents/nucleotide-archive-mcp/tools"},"ard":{"identifier":"urn:air::server:nucleotide-archive-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"nucleotide-archive-mcp","summary":"MCP server for searching European Nucleotide Archive (ENA) datasets. Find RNA-seq studies, retrieve metadata, and discover related publications to validate research hypotheses.","description":"# RNA Dataset Search - MCP Server\n\n[![BioContextAI - Registry](https://img.shields.io/badge/Registry-package?style=flat&label=BioContextAI&labelColor=%23fff&color=%233555a1&link=https%3A%2F%2Fbiocontext.ai%2Fregistry)](https://biocontext.ai/registry)\n[![Tests][badge-tests]][tests]\n[![Documentation][badge-docs]][documentation]\n\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/biocontext-ai/nucleotide_archive_mcp/test.yaml?branch=main\n[badge-docs]: https://img.shields.io/readthedocs/nucleotide_archive_mcp\n\nA Model Context Protocol (MCP) server for searching and accessing RNA sequencing datasets from the [European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena/browser/home). Find publicly available bulk RNA-seq and single-cell RNA-seq datasets to validate research hypotheses or reproduce published analyses.\n\n**Optimized for**: Human and mouse disease-related RNA-seq studies with support for bulk, single-cell, and spatial transcriptomics.\n\n## Features\n\n- **Disease-Focused Search**: Find datasets by disease, organism, and tissue type\n- **Advanced Technology Filtering**:\n  - Simple presets: bulk, single-cell, small-rna, ribo-seq, rna-all\n  - Granular control: Filter by 50+ library strategies (RNA-Seq, miRNA-Seq, ChIP-Seq, ATAC-seq, etc.)\n  - Source filtering: TRANSCRIPTOMIC, GENOMIC, METAGENOMIC, etc.\n- **Common Organism Names**: Use \"human\", \"mouse\", \"rat\" instead of scientific names\n- **Download Support**: Generate wget/curl scripts for downloading FASTQ files\n- **Study Metadata**: Retrieve comprehensive metadata including PubMed IDs\n- **Publication Links**: Discover datasets associated with PubMed publications\n- **Flexible Queries**: Build custom queries with multiple field conditions\n- **Field Discovery**: Explore available search and return fields\n- **Environment Configuration**: Customize API endpoints, timeouts, and logging via environment variables\n\n## Available Tools\n\nThe MCP server provides 10 specialized tools:\n\n### Search & Discovery\n…","publisher":{"name":"Malte Kuehl","url":null},"homepage":"https://nucleotide_archive_mcp.readthedocs.io/","repository":"https://github.com/biocontext-ai/nucleotide_archive_mcp","version":"0.0.7","license":"Apache License Version 2.0\n        Version 2.0, January 2004\n  …","protocols":["mcp"],"tags":["mcp"],"pricing":null,"endpoints":[{"url":"pypi:nucleotide-archive-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","publisherName":"pypi"}},"derived":{"capabilities":[{"slug":"research.academic","name":"Academic Research","confidence":0.825,"provenance":"derived"}],"categories":["research"],"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":"nucleotide-archive-mcp","registry":"pypi","observedAt":"2026-11-03T20:29:33.275Z","publishedAt":"2026-02-27T16:28:55.973685Z","latestVersion":"0.0.7"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"nucleotide-archive-mcp","url":"https://pypi.org/project/nucleotide-archive-mcp/","firstSeenAt":"2026-09-10T08:25:42.991Z","fetchedAt":"2026-11-03T20:27:57.025Z","normalizedAt":"2026-11-03T20:27:57.025Z"}]},"firstSeenAt":"2026-09-10T08:25:42.991Z","updatedAt":"2026-11-03T20:29:33.275Z"}