io.github.helena-bioinformaticsPublished by GitHub account helena-bioinformaticsv0.2.1Updated Oct 24, 2026
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
A read-only remote MCP server for searching a public PubMed-derived biomedical corpus and exploring citation and semantic neighborhoods around papers.
Web executable via Streamable HTTP. Remote servers run from the web runtime once configured in a workspace.
Paste this prompt into Claude Code, Codex, Cursor or another agent — or into SourceWeft chat. The agent reads this server's install guide, shows you its publisher, endpoint and sign-in, and adds it to your client once you agree. Keys never go into a command.
Read https://sourceweft.com/mcp/io.github.helena-bioinformatics%2Fnoodle/install.md and connect the MCP server it describes to my client. Before changing any config, show me its publisher, endpoint and sign-in method and wait for my OK. Never put an API key in a command or in a file I would commit; ask me where it should come from.Add this to your client's mcpServers config.
{
"mcpServers": {
"noodle-biomedical-literature-discovery": {
"type": "http",
"url": "https://api.helena.bio/noodle/v1/mcp"
}
}
}[DOI] [AllMCPs Verified] [OpenSSF Scorecard] [RRID]
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.
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.
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:
.difypkg;The companion Agent Skill is in
skills/noodle-biomedical-literature-discovery. It enables implicit,
task-first selection for requests such as:
Build the deterministic skill archive with:
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.
Python 3.12 is required.
Run the brand-blind contract audit with:
The benchmark contains 60 prompts that omit Noodle, Helena, and MCP.
It covers all six scientific routes plus negative and safety controls.
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
The persistent Research Resource Identifier is
RRID:SCR_028920. Cite the resource in a
methods section as Noodle (RRID:SCR_028920). Use the
version DOI 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 [email protected]
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.
Source: README.md at commit a0c92ae
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.
sortlimitqueryrequiredcursorGet publication details by PMID
Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.
pmidrequiredGet publication details by work ID
Retrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
work_idrequiredExplore a PMID literature neighborhood
Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.
pmidrequiredfrom_work_idExplore a work literature 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.
work_idrequiredfrom_work_idGet corpus summary
Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.
Takes no parameters.
Support Helena's free scientific infrastructure
Learn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.
Takes no parameters.
100% of the applicable checks met
How complete this listing is, computed from the registry entry, the endpoint and public sources. Not a rating of the server and not a statement that it is safe or working today: reachability is a dated check, and no installs or reviews go into the score.
python3 ops/package_agent_skill.pypython -m venv .venv. .venv/bin/activatepython -m pip install -r requirements-dev.lockpython -m pip install --no-deps -e .pytestruff check .ruff format --check .python benchmarks/agent-discovery/audit_skill.py