Noodle Biomedical Literature Discovery MCP server

online · 100% uptime

by helena-bioinformatics·io.github.helena-bioinformatics/noodle·v0.2.1

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Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.

A85/100grade A

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Safety scan

A85/100

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Noodle Biomedical Literature Discovery MCP tools (7)

write = sends, deletes, buys or posts

get_corpus_summaryFree
Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.
get_publication_detailsFree
Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.
get_publication_neighborhoodFree
Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.
get_work_detailsFree
Retrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
get_work_neighborhoodFree
Retrieve the bounded citation and semantic neighborhood around one Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
search_biomedical_literatureFree
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.
support_helenaFree
Learn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.

Public scan report

scanner v0.1.10 · 2026-10-30 · same rubric, same numbers if you re-run it

no findings

–Code scanremote-only server, no package to scann/a
Live reliabilityremote reachable in 1855ms20/20
Tool poisoning7 tool descriptions checked15/15
Auth qualityopen endpoint, read-only tools10/15
Maintenancelast push 59 days ago12/15
Maintainer identityregistry namespace matches repository owner7/10

Overall 85/100. Components that don't apply are left out of the denominator. Any critical finding is an F.Rubric Appeal a finding JSON

How Noodle Biomedical Literature Discovery MCP compares

Against every graded Web search MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score: 85/100; higher than 75% of 3,471 Web search servers
Tools: 7; the typical Web search server has 5
Tools that change things: 0%; typical: 0%. Fewer write tools means less an agent can break
Uptime: 100%; of our recent checks; the typical remote Web search server answers 100%
Response time: 113 ms; faster than 84% of 2,238 Web search servers

What its tools let an agent do: 7 read

Install Noodle Biomedical Literature Discovery MCP in Claude Code, Cursor or VS Code

claude mcp add --transport http noodle https://api.helena.bio/noodle/v1/mcp

Add to Cursor

What the publisher says

From the Noodle Biomedical Literature Discovery MCP repository's README, as published. We do not edit it. Read it on GitHub

Noodle Biomedical Literature Discovery MCP

The official public, read-only Model Context Protocol adapter for biomedical literature discovery from Helena Bioinformatics. 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

DOI, or PMCID;

search a public PubMed-derived biomedical corpus by natural language, PMID,

preserving edge types and graph provenance;

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

inspect corpus size, sources, freshness, coverage, and active graph metadata.

The seven published tools are searchbiomedicalliterature, getpublicationdetails, getworkdetails, getpublicationneighborhood, getworkneighborhood, getcorpussummary, 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:

contract supported by the hosted service;

Dify, including a reproducible .difypkg;
n8n, using the exact stateless MCP JSON-RPC

wrapper; and

Galaxy, with a Planemo-linted ToolShed

Python Script node and prepared Hub listing; and

KNIME Analytics Platform, with a table-to-MCP

Cytoscape GraphML workflow; and

Google Colab and Kaggle notebooks, plus a

for a Folklore-to-Noodle literature workflow.

the companion Galaxy Training Network tutorial

The companion Agent Skill is in skills/noodle-biomedical-literature-discovery. It enables implicit, task-first selection for requests such as:

similarity.”

“Find source-linked papers about BRCA1 homologous recombination.”
“What publication is PMID 35008774?”
“Show papers related to this article through citations and semantic

“Walk two bounded hops from this work ID and preserve the edge types.”

Build the deterministic skill archive with:

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.

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 .

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

Noodle Biomedical Literature Discovery MCP: common questions

Is Noodle Biomedical Literature Discovery MCP server safe?: Yes, by our scan: it is graded A (85/100). Read the Noodle Biomedical Literature Discovery MCP safety report
How do I install Noodle Biomedical Literature Discovery MCP?: It runs remotely at api.helena.bio. Add it to Claude Code, Cursor, VS Code or Claude Desktop with the snippets above, or call it through the mcp.market gateway without installing anything.
Does Noodle Biomedical Literature Discovery MCP need an API key?: Not as far as the registry entry and our scan can tell: no credentials are declared or required.
Is Noodle Biomedical Literature Discovery MCP maintained?: The last commit was 66 days ago (2026-09-01). The latest release is v0.2.1.
Is Noodle Biomedical Literature Discovery MCP up?: 100% of our last 28 checks got an answer. We check remote servers about four times a day.
What can I use instead of Noodle Biomedical Literature Discovery MCP?: Servers from other publishers that do the same job: Arxiv MCP server, Semantic Scholar MCP Server and PubMed Search MCP server.
How does Noodle Biomedical Literature Discovery MCP compare with other Web search MCP servers?: safety score 85/100 (higher than 75% of 3,471 Web search servers); tools 7 (the typical Web search server has 5); tools that change things 0% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.

Alternatives to Noodle Biomedical Literature Discovery MCP

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Run it through the gateway

With the gateway added, ask your agent for it by name:

agent prompt

call io.github.helena-bioinformatics/noodle → get_corpus_summary

Free per call. Metered, capped by your key, logged for reliability.

Add the gateway (gw.mcp.market)

Rating: —
Safety grade: A · 85/100
Stars: 0
Downloads/wk: –
Price: Free
Licence: Apache-2.0
Transport: Remote
Uptime: 100% · 28/28 checks
Version: 0.2.1
Category: Web search
Last release: 2026-09-01

Endpoint

https://api.helena.bio/noodle/v1/mcp

streamable-http

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