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Oliver's mTOR Atlas

io.github.open-mtor-atlas/mtor-atlas · v1.3.0

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

MCPremotelocal · npmno credentialsHealth

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Last check

Reachable, 13 tools, protocol 2025-06-18 · checked 2026-10-17

Test & rating

A 95/100

What it does: 13 tools · 13 read, 0 write · Health, Developer tools

Test call list_questions: worked (1,413 ms)

How the rating is made
  • Answers without login: +30
  • Speed of first answer: +10
  • Lists tools: +10
  • Tool descriptions: +15
  • Parameter descriptions: +5
  • Read/write annotations: +5
  • Safe test call: +20
  • More than 80 tools: 0

Tested 2026-10-17. Fixed rules, no AI model. Grade A needs a successful real call.

Install

Remote URL
https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp
Package
registry:   npm
identifier: mtor-atlas-mcp
version:    1.3.0
transport:  stdio

Tools

13 tools listed at last check
  • atlas_about Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset. derived_counts adds figures computed from the relations (flagged contested, with conflicting studies, either) so they can be compared with find_contradictions.
  • search_studies 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,
  • get_study 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.
  • search_entities 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.
  • get_entity 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.
  • find_relations 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.
  • get_relation One pathway relation by ID (e.g. "RHEB-MTORC1"): mechanism, boundary conditions, confidence, supporting and conflicting studies.
  • evidence_between 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_i
  • find_contradictions 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 and shows related relations named in its text. Paged:
  • list_questions 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.
  • get_question 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.
  • search_authors 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.
  • get_author 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.

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