# Noodle Biomedical Literature Discovery MCP [Verified] [Health: Active]

**Category:** 🧬 Biology & Bioinformatics  
**Repository:** https://github.com/helena-bioinformatics/noodle-mcp  
**GitHub Stars:** 0  
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**Directory Page:** https://allmcps.com/mcp/noodle-biomedical-literature-discovery-mcp

## Description
Official public, read-only Model Context Protocol server from Helena Bioinformatics for biomedical literature discovery. Agents can search PubMed and scholarly research, resolve PMID, DOI, and PMCID identifiers, inspect publication metadata, find related papers, traverse bounded citation graphs, explore semantic literature neighborhoods, and check corpus coverage. Use the hosted Streamable HTTP endpoint https://api.helena.bio/noodle/v1/mcp; no npm or npx package is required.

## Tools
Capabilities this server exposes over MCP:

- **search_biomedical_literature** — Semantically search Noodle's public PubMed-derived biomedical corpus. Include known PMID, DOI, or PMCID identifiers in the query so they can act as exact anchors. Results are for literature discovery and professional review, not diagnosis or treatment.
- **get_publication_details** — Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.
- **get_work_details** — Retrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
- **get_publication_neighborhood** — Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.
- **get_work_neighborhood** — Retrieve the bounded citation and semantic neighborhood around one Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
- **get_corpus_summary** — Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.
- **support_helena** — Learn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.

## Claude Desktop Quick Installation
Remote MCP endpoint (confidence: high). Install path detected from listing signals. Add as a URL/SSE server in your client:

```json
"mcpServers": {
  "noodle-biomedical-literature-discovery-mcp": {
    "url": "https://api.helena.bio/noodle/v1/mcp"
  }
}
```

## Documentation

## What Noodle Biomedical Literature Discovery MCP does

Noodle Biomedical Literature Discovery MCP MCP server exposes a public, read-only literature discovery service from Helena Bioinformatics. It is intended for finding and inspecting biomedical publications rather than modifying records or submitting private material. The searchable collection is derived from PubMed and can be queried with natural-language topics or identifiers such as PMID, DOI, and PMCID.

The service supports two kinds of work: retrieving information about known publications and discovering additional papers. An agent can resolve an identifier, inspect publication metadata, identify related works, and follow bounded citation or semantic relationships. Corpus-level metadata is also available for checking sources, freshness, size, coverage, and active graph information.

## How it works

Clients connect to the hosted Streamable HTTP endpoint at `https://api.helena.bio/noodle/v1/mcp`. Any MCP client with remote Streamable HTTP support can use the service. No local npm or npx package is required, and the public service does not require or accept an account, API key, patient data, or private content.

A typical exploration begins with a PMID or Noodle work ID. The client requests one bounded neighborhood at a time, retains the returned work identifiers, and can continue from those identifiers for further exploration. Results preserve edge types and graph provenance. Search ranking, citation distance, semantic similarity, co-mention, and graph distance are discovery signals; they are not evidence of causality, scientific validity, diagnosis, or treatment effectiveness.

## Tools and capabilities

The Noodle Biomedical Literature Discovery MCP MCP server publishes seven actions:

- `search_biomedical_literature` searches the public biomedical corpus.
- `get_publication_details` retrieves source-linked details by PMID.
- `get_work_details` retrieves details by Noodle work ID.
- `get_publication_neighborhood` explores bounded relationships from a publication.
- `get_work_neighborhood` explores bounded relationships from a work.
- `get_corpus_summary` reports corpus and graph metadata.
- `support_helena` is a separate, explicit opt-in information action.

These capabilities support workflows such as finding papers on a gene or disease, resolving a citation identifier, comparing nearby literature, and walking a constrained graph while retaining relationship types. The repository also includes guidance and integrations for platforms including Dify, n8n, Galaxy, KNIME, notebooks, and Cytoscape, but the core service is accessed through MCP.

## Limitations and notes

Noodle Biomedical Literature Discovery MCP MCP server is read-only. It should not be used to send patient information, clinical records, credentials, private case details, or private uploaded content to the public endpoint or issue tracker. The graph must be traversed in bounded steps, with a visited-ID set and a stop condition when no neighborhood is returned.

The service helps discover and organize research; it does not establish that a paper is scientifically valid, that two works have a causal relationship, or that a finding supports a diagnosis or treatment. Developers building research agents should present the returned source links and distinguish discovery signals from conclusions. The project is distributed under the Apache License 2.0.

_Full upstream README: https://allmcps.com/mcp/noodle-biomedical-literature-discovery-mcp/readme_