Oliver's mTOR Atlas

by open-mtor-atlas · remote · local (npm) · no sign-in to list tools · v1.3.3 · published by GitHub user open-mtor-atlas

Evidence-labelled mTOR research: studies, entities, pathway claims, contradictions, open questions.

Changes · 2

Compare Registry entry

13 tools: 2 change things and 11 only read.

Scanned Oct 21, 2026

Deletes or cancels0Claude Code: deny
Can't be undone0Claude Code: ask
Changes things2Claude Code: ask: see these tools
Only reads11Claude 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 mtor-atlas https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp

Tools

Open a tool for its reasons and full description. Descriptions are the publisher's own words, shown as they are.

13 tools

Changes things 2Creates or changes something that can be changed back.Claude Code: ask

atlas_aboutDataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset.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
Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset. When the Atlas does not report the contested and conflicting counts itself, derived_counts adds them, computed from the relations, so they can be compared with find_contradictions.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: About the Atlas
evidence_betweenDirect curated relations between two entities (either direction) with full cards for the supporting and conflicting studies.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
Direct curated relations between two entities (either direction) with full cards for the supporting and conflicting studies. Answers questions such as "what is the evidence that A acts on B?". A study that repeats within the answer is sent in full once and afterwards as a short card with full_card_in.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Evidence between two entities

Only reads 11Looks things up and changes nothing.Claude Code: allow

find_contradictionsRelations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence.No findings
Why it is in this group
- The name "find_contradictions" says "find": a word for reading.
Description, as the server wrote it
Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. status says which; breakdown splits the total. A contested relation with no conflicting study listed is flagged conflicting_studies_missing; relations named in its note or boundary are shown in named_in_text (a mention is not evidence). Paged: pass next_offset as offset for the rest. Optionally limited to one entity.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Find contested claims
find_relationsSigned, evidence-linked pathway relations (claims such as "Rheb activates mTORC1").No findings
Why it is in this group
- The name "find_relations" says "find": a word for reading.
Description, as the server wrote it
Signed, evidence-linked pathway relations (claims such as "Rheb activates mTORC1"). Filter by an entity on either end, by source/target, effect, contested status or minimum strength of the best supporting evidence.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Find pathway relations
get_authorOne profiled author by profile id ("claudio-de-virgilio"), full name, author-list form or ORCID: lab, role, profile URL and short cards of their studies in the Atlas.No findings
Why it is in this group
- The name "get_author" says "get": a word for reading.
Description, as the server wrote it
One profiled author by profile id ("claudio-de-virgilio"), full name, author-list form or ORCID: lab, role, profile URL and short cards of their studies in the Atlas.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Get one author
get_entityOne entity (gene/protein, complex, drug, disease, process...) with its linked studies as short cards (first studies_limit) and every pathway relation it takes part in as a one-line…No findings
Why it is in this group
- The name "get_entity" says "get": a word for reading.
Description, as the server wrote it
One entity (gene/protein, complex, drug, disease, process...) with its linked studies as short cards (first studies_limit) and every pathway relation it takes part in as a one-line claim. Accepts an id, a name or a synonym.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Get one entity
get_questionOne open or frontier question by ID (e.g.No findings
Why it is in this group
- The name "get_question" says "get": a word for reading.
Description, as the server wrote it
One open or frontier question by ID (e.g. "H1", "F2"): the gap, what changed, what is still open, how it could be tested, linked studies.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Get one question
get_relationOne pathway relation by ID (e.g.No findings
Why it is in this group
- The name "get_relation" says "get": a word for reading.
Description, as the server wrote it
One pathway relation by ID (e.g. "RHEB-MTORC1"): mechanism, boundary conditions, confidence, supporting and conflicting studies.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Get one relation
get_studyFull record for one study by Atlas ID (e.g.No findings
Why it is in this group
- The name "get_study" says "get": a word for reading.
Description, as the server wrote it
Full record for one study by Atlas ID (e.g. "SAB1994"), PMID, DOI or PMCID: abstract excerpt, extracted findings, linked entities, the relations it supports or contradicts, related open questions.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Get one study
list_questionsThe Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions.No findings
Why it is in this group
- The name "list_questions" says "list": a word for reading.
Description, as the server wrote it
The Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions. Paged. By default still_open is shortened at a sentence boundary (still_open_truncated); get_question has the full text, or pass brief=false.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: List open questions
search_authorsPeople in the Atlas by full name ("Claudio De Virgilio"), author-list form ("De Virgilio C"), ORCID or lab.No findings
Why it is in this group
- The name "search_authors" says "search": a word for reading.
Description, as the server wrote it
People in the Atlas by full name ("Claudio De Virgilio"), author-list form ("De Virgilio C"), ORCID or lab. results are authors with a profile page (full name, ORCID, lab, their study IDs); in_author_lists are matching names in study author lists without a profile.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Search authors
search_entitiesFind genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym.No findings
Why it is in this group
- The name "search_entities" says "search": a word for reading.
Description, as the server wrote it
Find genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym. Each result says where it matched (match_field: name, synonym or description); use match="name" to leave out description-only hits.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Search entities
search_studiesSearch the curated studies by keywords, optionally filtered by evidence code, a linked entity (gene, drug, disease...) and year range.No findings
Why it is in this group
- The name "search_studies" says "search": a word for reading.
Description, as the server wrote it
Search the curated studies by keywords, optionally filtered by evidence code, a linked entity (gene, drug, disease...) and year range. Searches title, finding, authors (author-list form "Sabatini DM" and full names of profiled authors), PMID, DOI, PMCID, linked entities and their synonyms, journal, model system and the abstract excerpt. A query that is a PMID or DOI returns that study. Returns summary records with evidence codes and URLs.
Annotations the server declares
- readOnlyHint: true
- destructiveHint: false
- openWorldHint: false
- idempotentHint: true
- title: Search studies

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 1.3.3. Values in angle brackets are yours to fill in.

claude mcp add --transport http mtor-atlas https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp

Run in a terminal.

Claude Code permissions

Allow the reads, ask before a change, deny the deletes. Paste into .claude/settings.json.

.claude/settings.json

{
  "permissions": {
    "allow": [
      "mcp__mtor-atlas__search_studies",
      "mcp__mtor-atlas__get_study",
      "mcp__mtor-atlas__search_entities",
      "mcp__mtor-atlas__get_entity",
      "mcp__mtor-atlas__find_relations",
      "mcp__mtor-atlas__get_relation",
      "mcp__mtor-atlas__find_contradictions",
      "mcp__mtor-atlas__list_questions",
      "mcp__mtor-atlas__get_question",
      "mcp__mtor-atlas__search_authors",
      "mcp__mtor-atlas__get_author"
    ],
    "ask": [
      "mcp__mtor-atlas__atlas_about",
      "mcp__mtor-atlas__evidence_between"
    ],
    "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 mtor-atlas. Review it before you use it.

Keep track

Get told when this server's tools change: a new tool, a new description, a new class.

https://anlyon.dev/servers/io.github.open-mtor-atlas/mtor-atlas/changes.xml

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Anlyon alternative

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Source: MCP Registry · repository. Synced Oct 21, 2026, 18:43 UTC.

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