io.github.open-mtor-atlas/mtor-atlas

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Les 13 outils

• atlas_about≈ 135 tokens

  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.

  Paramètres, retour & exemple (0)

  Exemple d'appel

  {"name": "atlas_about", "arguments": {}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• evidence_between≈ 218 tokens

  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.

  Paramètres, retour & exemple (3)

  Paramètres

  • a · string · requis
  • b · string · requis
  • dedupe · boolean · optionnel
    Send a repeated study in full only once. Pass false for a full card every time.

  Exemple d'appel

  {"name": "evidence_between", "arguments": {"a": "texte", "b": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• find_contradictions≈ 397 tokens

  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.

  Paramètres, retour & exemple (6)

  Paramètres

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

  Exemple d'appel

  {"name": "find_contradictions", "arguments": {"brief": true, "limit": 1, "dedupe": true, "entity": "texte", "offset": 1, "only_contested": true}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• find_relations≈ 366 tokens

  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.

  Paramètres, retour & exemple (8)

  Paramètres

  • limit · integer · optionnel
    Maximum 50; a larger value is capped at 50.
  • effect · string · optionnel · activates | inhibits | binds | recruits | required-for | context-dependent | no-effect
  • entity · string · optionnel
    Entity on either end of the relation
  • offset · integer · optionnel
    For the next page: pass next_offset from the previous answer.
  • source · string · optionnel
  • target · string · optionnel
  • contested_only · boolean · optionnel
    Only relations marked contested or with conflicting studies
  • strongest_at_least · string · optionnel · S | H | A | M | R | PP | RT
    Keep relations whose best supporting study is at least this code in the order S > H > A > M

  Exemple d'appel

  {"name": "find_relations", "arguments": {"limit": 1, "effect": "activates", "entity": "texte", "offset": 1, "source": "texte", "target": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• get_author≈ 166 tokens

  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.

  Paramètres, retour & exemple (2)

  Paramètres

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

  Exemple d'appel

  {"name": "get_author", "arguments": {"id": "texte", "author": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• get_entity≈ 211 tokens

  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.

  Paramètres, retour & exemple (3)

  Paramètres

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

  Exemple d'appel

  {"name": "get_entity", "arguments": {"id": "texte", "entity": "texte", "studies_limit": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• get_question≈ 126 tokens

  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.

  Paramètres, retour & exemple (1)

  Paramètres

  • id · string · requis

  Exemple d'appel

  {"name": "get_question", "arguments": {"id": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• get_relation≈ 124 tokens

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

  Paramètres, retour & exemple (1)

  Paramètres

  • id · string · requis

  Exemple d'appel

  {"name": "get_relation", "arguments": {"id": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• get_study≈ 185 tokens

  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.

  Paramètres, retour & exemple (3)

  Paramètres

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

  Exemple d'appel

  {"name": "get_study", "arguments": {"id": "texte", "sid": "texte", "study_id": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• list_questions≈ 304 tokens

  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.

  Paramètres, retour & exemple (5)

  Paramètres

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

  Exemple d'appel

  {"name": "list_questions", "arguments": {"kind": "open-question", "brief": true, "limit": 1, "query": "texte", "offset": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• search_authors≈ 263 tokens

  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.

  Paramètres, retour & exemple (3)

  Paramètres

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

  Exemple d'appel

  {"name": "search_authors", "arguments": {"query": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• search_entities≈ 319 tokens

  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.

  Paramètres, retour & exemple (5)

  Paramètres

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

  Exemple d'appel

  {"name": "search_entities", "arguments": {"query": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

• search_studies≈ 434 tokens

  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.

  Paramètres, retour & exemple (7)

  Paramètres

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

  Exemple d'appel

  {"name": "search_studies", "arguments": {"limit": 1, "query": "texte", "entity": "texte", "offset": 1, "year_to": 1, "year_from": 1}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}]}

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Source

https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp