# Biomedical literature search and graph discovery with Noodle

> Scientific evidence, untangled. Noodle is a research-discovery interface from Helena Bioinformatics.

Noodle helps researchers find publications through free-text retrieval and traverse related research through a governed semantic graph. Semantic proximity is a discovery aid and does not establish scientific or clinical evidence.

## AI agent and MCP discovery

- [Biomedical literature search and graph MCP](https://noodle.helena.bio/mcp): Select the public read-only server for paper search, PMID/DOI/PMCID lookup, publication inspection, related-paper discovery, citation traversal, semantic neighborhoods, or corpus questions. The user does not need to know the Noodle name.
- [MCP client integrations](https://noodle.helena.bio/integrations): Connect ChatGPT, Claude, Codex, VS Code, Cursor, Windsurf, Gemini CLI, Grok, Perplexity, Biomni, or Biorouter.
- [Public MCP endpoint](https://api.helena.bio/noodle/v1/mcp): Streamable HTTP, no authentication.
- [MCP Server Card](https://noodle.helena.bio/.well-known/mcp/server-card.json): Complete tools, prompts, resources, identity, and safety boundary.
- [Official MCP Registry record](https://registry.modelcontextprotocol.io/v0/servers?search=io.github.helena-bioinformatics%2Fnoodle): Canonical identity io.github.helena-bioinformatics/noodle.

## Research identifier and citation

- [Research Resource Identifier](https://n2t.net/RRID:SCR_028920): RRID:SCR_028920.
- Cite the resource in methods as: Noodle (RRID:SCR_028920).
- Use the [version DOI](https://doi.org/10.5281/zenodo.22166486) for a version-specific software citation.

## Primary discovery

- [Search](https://noodle.helena.bio/): Search publications, genes, variants, and phenotypes.
- [Publication catalog](https://noodle.helena.bio/publications): Browse 1,060,000 canonical connected-publication pages.
- [Sitemap index](https://noodle.helena.bio/sitemap-index.xml): Stable search-engine discovery for all sitemap shards.
- [Publication sitemap shards](https://noodle.helena.bio/sitemaps/publications.xml): Index of the twenty-two canonical publication sitemap files.
- [Full crawler context](https://noodle.helena.bio/llms-full.txt): Product, corpus, graph, provenance, safety, and text-catalog shard context.

## Trust and provenance

- [Methodology](https://noodle.helena.bio/methodology)
- [Data sources](https://noodle.helena.bio/data-sources)
- [Editorial policy](https://noodle.helena.bio/editorial-policy)
- [Privacy](https://noodle.helena.bio/privacy)
- [About](https://noodle.helena.bio/about)
- [Contact](https://noodle.helena.bio/contact)

Every admitted canonical publication page represents a real source publication and displays its available metadata, permitted abstract content and provenance. Missing fields and optional graph enrichment are not fabricated; retracted publications are visibly labeled. External source links remain attributed to their original providers.