Oliver's mTOR Atlas

Connect Remote server

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

{
  "mcpServers": {
    "mtor-atlas": {
      "url": "https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp"
    }
  }
}

{
  "servers": {
    "mtor-atlas": {
      "type": "http",
      "url": "https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp"
    }
  }
}

Settings > Connectors > Add custom connector
URL: https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp

Tools 13 found in our last check

• atlas_about

  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.

• 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 thei…

• 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…

• 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. conflict carries WHY the studies disagree (Opposing result / Different context / Field dispute) with its basis. A contested r…

• 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. If the name fits several people or has no profile page, the answer lists candidates (resolved: false) instead.

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