Oliver's mTOR Atlas

Measured conclusion: Deep-tested. L2 outcome: tools_ok.

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

Add to your agent

Copy this into your MCP client config:

{
  "mcpServers": {
    "Oliver's mTOR Atlas": {
      "url": "https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp",
      "transport": "streamable-http"
    }
  }
}

Measured tools (13)

• atlas_about read-only

  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.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• search_studies read-only

  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.

  Parameters:

  • limit — integer — Maximum 50; a larger value is capped at 50.
  • query — string — Keywords, e.g. "rapamycin lifespan mice", a person ("Claudio De Virgilio"), a PMID or a DOI. Omit to list by filters only.
  • entity — string — Only studies linked to this entity (name, synonym or id), e.g. "Rheb".
  • offset — integer — For the next page: pass next_offset from the previous answer.
  • year_to — integer
  • year_from — integer
  • evidence_code — array — Keep only these evidence codes, e.g. ["H","S"] for human evidence.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• get_study read-only

  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.

  Parameters:

  • id — string — Alias of sid.
  • sid — string — Atlas study ID ("SAB1994"), PMID ("23716719"), DOI or PMCID
  • study_id — string — Alias of sid.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• search_entities read-only

  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.

  Parameters:

  • query (required) — string — Name or synonym, e.g. "raptor", "sirolimus"
  • type — string — Optional type filter, e.g. "Drug", "Gene/Protein", "Disease"
  • limit — integer — Maximum 100; a larger value is capped at 100.
  • match — string — "any" also searches descriptions; "name" searches names and synonyms only.
  • offset — integer — For the next page: pass next_offset from the previous answer.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• get_entity read-only

  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.

  Parameters:

  • id — string — Alias of entity.
  • entity — string — e.g. "mTORC1", "Rheb", "rapamycin"
  • studies_limit — integer — Maximum 50; a larger value is capped at 50.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• find_relations read-only

  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.

  Parameters:

  • limit — integer — Maximum 50; a larger value is capped at 50.
  • effect — string
  • entity — string — Entity on either end of the relation
  • offset — integer — For the next page: pass next_offset from the previous answer.
  • source — string
  • target — string
  • contested_only — boolean — Only relations marked contested or with conflicting studies
  • strongest_at_least — string — Keep relations whose best supporting study is at least this code in the order S > H > A > M

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• get_relation read-only

  One pathway relation by ID (e.g. "RHEB-MTORC1"): mechanism, boundary conditions, confidence, supporting and conflicting studies.

  Parameters:

  • id (required) — string

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• evidence_between read-only

  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.

  Parameters:

  • a (required) — string
  • b (required) — string
  • dedupe — boolean — Send a repeated study in full only once. Pass false for a full card every time.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• find_contradictions read-only

  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.

  Parameters:

  • brief — boolean — Shorten the long boundary and note text (text_truncated is set); get_relation has the full text.
  • limit — integer — Maximum 50; a larger value is capped at 50.
  • dedupe — boolean — Send a repeated study in full only once. Pass false for a full card every time.
  • entity — string
  • offset — integer — For the next page: pass next_offset from the previous answer.
  • only_contested — boolean — Keep only relations the Atlas flags contested, not those that merely carry conflicting studies.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• list_questions read-only

  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.

  Parameters:

  • kind — string
  • brief — boolean — Shorten still_open; false returns the full text.
  • limit — integer — Maximum 50; a larger value is capped at 50.
  • query — string — Keywords to find questions by their title, gap, hypothesis or what is still open, e.g. "rapamycin immune".
  • offset — integer — For the next page: pass next_offset from the previous answer.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• get_question read-only

  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.

  Parameters:

  • id (required) — string

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• search_authors read-only

  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.

  Parameters:

  • query (required) — string — A name, ORCID or lab, e.g. "Sabatini", "Claudio De Virgilio", "Fribourg"
  • limit — integer — Maximum 50; a larger value is capped at 50.
  • offset — integer — For the next page: pass next_offset from the previous answer.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• get_author read-only

  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.

  Parameters:

  • id — string — Alias of author.
  • author — string — e.g. "Claudio De Virgilio", "De Virgilio C", "claudio-de-virgilio"

  Hints: read-only yes · destructive no · idempotent yes · open-world no

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