Noodle Biomedical Literature Discovery MCP
by helena-bioinformatics · remote · no sign-in to list tools · v0.2.1 · published by GitHub user helena-bioinformatics
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
7 tools: 1 change things and 6 only read.
Scanned Oct 21, 2026
- Deletes or cancels0Claude Code: deny
- Can't be undone0Claude Code: ask
- Changes things1Claude Code: ask: see these tools
- Only reads6Claude Code: allow: see these tools
No check matched anything in the tool definitions. No finding is not a safety guarantee. How the checks work.
claude mcp add --transport http noodle https://api.helena.bio/noodle/v1/mcpTools
Open a tool for its reasons and full description. Descriptions are the publisher's own words, shown as they are.
7 tools
Changes things 1Claude Code: ask
support_helenaLearn about the separate Helena Good MCP.No findings
Why it is in this group
- Nothing in its name or description says what it does, so it is counted as a write.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.
Description, as the server wrote it Learn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: false
- readOnlyHint: true
- title: Support Helena's free scientific infrastructure
Only reads 6Claude Code: allow
get_corpus_summaryReturn public corpus coverage, source, freshness, and count metadata.No findings
Why it is in this group
- The name "get_corpus_summary" says "get": a word for reading.
Description, as the server wrote it Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: false
- readOnlyHint: true
- title: Get corpus summary
get_publication_detailsRetrieve one complete public bibliographic record by PMID after search.No findings
Why it is in this group
- The name "get_publication_details" says "get": a word for reading.
Description, as the server wrote it Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: false
- readOnlyHint: true
- title: Get publication details by PMID
get_publication_neighborhoodRetrieve the bounded citation and semantic neighborhood around one PMID.No findings
Why it is in this group
- The name "get_publication_neighborhood" says "get": a word for reading.
Description, as the server wrote it Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: false
- readOnlyHint: true
- title: Explore a PMID literature neighborhood
get_work_detailsRetrieve one complete public bibliographic record by Noodle work identifier.No findings
Why it is in this group
- The name "get_work_details" says "get": a word for reading.
Description, as the server wrote it Retrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: false
- readOnlyHint: true
- title: Get publication details by work ID
get_work_neighborhoodRetrieve the bounded citation and semantic neighborhood around one Noodle work identifier.No findings
Why it is in this group
- The name "get_work_neighborhood" says "get": a word for reading.
Description, as the server wrote it Retrieve the bounded citation and semantic neighborhood around one Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: false
- readOnlyHint: true
- title: Explore a work literature neighborhood
search_biomedical_literatureSemantically search Noodle's public PubMed-derived biomedical corpus.No findings
Why it is in this group
- The name "search_biomedical_literature" says "search": a word for reading.
Description, as the server wrote it 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.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: false
- readOnlyHint: true
- title: Search biomedical literature
This is not a safety rating, and no finding is not a safety guarantee. The groups and findings come from fixed checks of the tool definitions the server returned on the date shown, not from its code or what it does when called. How the checks work.
Install
Pinned to version 0.2.1. Values in angle brackets are yours to fill in.
claude mcp add --transport http noodle https://api.helena.bio/noodle/v1/mcpRun in a terminal.
Claude Code permissions
Allow the reads, ask before a change, deny the deletes. Paste into .claude/settings.json.
{
"permissions": {
"allow": [
"mcp__noodle__search_biomedical_literature",
"mcp__noodle__get_publication_details",
"mcp__noodle__get_work_details",
"mcp__noodle__get_publication_neighborhood",
"mcp__noodle__get_work_neighborhood",
"mcp__noodle__get_corpus_summary"
],
"ask": [
"mcp__noodle__support_helena"
],
"deny": []
}
}Tools that only read are allowed, tools that change things ask first, tools that delete or cancel are denied. It assumes the server is installed as noodle. Review it before you use it.