Noodle Biomedical Literature Discovery MCP
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
Open source Repository Open in the app JSON README (API)
About
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
Details
- Kind
- MCP servers
- Topic
- No topic detected
- Publisher
- helena-bioinformatics
- Origin
- official
- Category
- ferramentas
- Transport
- http
- Version
- 0.2.1
- Last push
- 2026-09-01T00:33:07Z
- Repository state
- ativo
- Language
- Python
- License
- Apache-2.0
- Added
- 2026-08-29 15:00:29
- Updated
- 2026-08-30 14:01:02
- Origin id
io.github.helena-bioinformatics/noodle
README
# Noodle Biomedical Literature Discovery MCP [](https://doi.org/10.5281/zenodo.22166486) [](https://allmcps.com/mcp/noodle-biomedical-literature-discovery-mcp?verify=930d811d-1fd8-4117-8280-1c6eac1a2ca3) [](https://scorecard.dev/viewer/?uri=github.com/helena-bioinformatics/noodle-mcp) [](https://n2t.net/RRID:SCR_028920) The official public, read-only Model Context Protocol adapter for biomedical literature discovery from [Helena Bioinformatics](https://www.helena.bio). Agents can select it from a user task even when the user does not know the Noodle brand. Public endpoint: `https://api.helena.bio/noodle/v1/mcp` Official Registry identity: `io.github.helena-bioinformatics/noodle` No account, API key, patient data, or private content is required or accepted. ## What agents can do - search a public PubMed-derived biomedical corpus by natural language, PMID, DOI, or PMCID; - retrieve source-linked publication records by PMID or Noodle work ID; - traverse bounded citation and semantic neighborhoods from a publication; - continue graph exploration through returned work identifiers while preserving edge types and graph provenance; - inspect corpus size, sources, freshness, coverage, and active graph metadata. The seven published tools are `search_biomedical_literature`, `get_publication_details`, `get_work_details`, `get_publication_neighborhood`, `get_work_neighborhood`, `get_corpus_summary`, and the separate explicit opt-in `support_helena` information action. ## Connect Any MCP client that supports remote Streamable HTTP can use the endpoint. Exact recipes for ChatGPT, Claude, Codex, VS Code, Cursor, Windsurf, Gemini CLI, Grok, Perplexity, Microsoft Copilot Studio, Biomni, and Biorouter live under `registry/platforms` and `integrations`. Ready-to-use ecosystem packages are included for: - [Dify](integrations/dify/README.md), including a reproducible `.difypkg`; - [n8n](integrations/n8n/README.md), using the exact stateless MCP JSON-RPC contract supported by the hosted service; - [Galaxy](integrations/galaxy/README.md), with a Planemo-linted ToolShed wrapper; and - [KNIME Analytics Platform](integrations/knime/README.md), with a table-to-MCP Python Script node and prepared Hub listing; and - [Google Colab and Kaggle notebooks](integrations/notebooks/README.md), plus a [Cytoscape GraphML workflow](integrations/cytoscape/README.md); and - the companion [Galaxy Training Network tutorial](integrations/galaxy-training-network/README.md) for a Folklore-to-Noodle literature workflow. The companion Agent Skill is in `skills/noodle-biomedical-literature-discovery`. It enables implicit, task-first selection for requests such as: - “Find source-linked papers about BRCA1 homologous recombination.” - “What publication is PMID 35008774?” - “Show papers related to this article through citations and semantic similarity.” - “Walk two bounded hops from this work ID and preserve the edge types.” Build the deterministic skill archive with: ```bash python3 ops/package_agent_skill.py ``` ## Graph boundary Start from a resolved PMID or work ID and request one bounded neighborhood at a time. Report edges exactly as returned, keep a visited-ID set, and stop at a missing neighborhood. Search rank, citation proximity, semantic similarity, co-mention, and graph distance are discovery signals. They do not establish causality, scientific validity, diagnosis, or treatment. ## Development Python 3.12 is required. ```bash python -m venv .venv . .venv/bin/activate python -m pip install -r requirements-dev.lock python -m pip install --no-deps -e . pytest ruff check . ruff format --check . ``` Run the brand-blind contract audit with: ```bash python benchmarks/agent-discovery/audit_skill.py ``` The benchmark contains 60 prompts that omit `Noodle`, `Helena`, and `MCP`. It covers all six scientific routes plus negative and safety controls. ## Agent Plugin and Kiro Power This repository is also a portable Agent Plugin and Kiro Power. `plugin.json` provides brand-blind activation keywords, the existing Agent Skill supplies the scientific routing and safety boundary, and `mcp.json` connects directly to the canonical hosted Streamable HTTP endpoint. The Power does not proxy, repackage, or reimplement Noodle. Privacy policy: https://noodle.helena.bio/privacy ## Cite Noodle The persistent Research Resource Identifier is [`RRID:SCR_028920`](https://n2t.net/RRID:SCR_028920). Cite the resource in a methods section as **Noodle (RRID:SCR_028920)**. Use the [version DOI](https://doi.org/10.5281/zenodo.22166486) when a version-specific software citation is also needed. The RRID identifies the resource across publications, while the DOI identifies the archived 0.2.0 release. Support: https://noodle.helena.bio/contact or `contact@helena.bio` ## Public resources - Hands-on tutorial: https://github.com/helena-bioinformatics/noodle-mcp/blob/main/docs/tutorials/biomedical-literature-discovery-and-graph-traversal.md - Connector and agent-selection guide: https://noodle.helena.bio/mcp - Client integrations: https://noodle.helena.bio/integrations - Server Card: https://noodle.helena.bio/.well-known/mcp/server-card.json - Official Registry: https://registry.modelcontextprotocol.io/v0/servers?search=io.github.helena-bioinformatics%2Fnoodle - Citable release: https://doi.org/10.5281/zenodo.22166486 - Software Heritage archive request: https://archive.softwareheritage.org/api/1/origin/save/2457442/ - Software Heritage snapshot: https://archive.softwareheritage.org/swh:1:snp:09b8fb7c64de15487e873b4f77e3e4b57abc02fb/ - Methodology: https://noodle.helena.bio/methodology ## License and security Apache License 2.0. Report vulnerabilities privately as described in `SECURITY.md`. Do not submit patient, private case, clinical-record, credential, or private uploaded content to the public service or issue tracker.