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Oliver's mTOR Atlas

io.github.open-mtor-atlas/mtor-atlas
科学・工学 検索・リサーチ 公開・接続可能 MCP 2025-11-25

このMCPでできること

Provides an evidence-labelled knowledge base of mTOR entities, pathway relations, studies, contradictions, and open research questions.

機能

ツール

11 ツール
atlas_about
About the Atlas
Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', 'properties': {}}
evidence_between
Evidence between two entities
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?".
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'required': ['a', 'b'], 'properties': {'a': {'type': 'string'}, 'b': {'type': 'string'}}}
find_contradictions
Find contested claims
Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. Optionally limited to one entity.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'properties': {'limit': {'type': 'integer', 'default': 20, 'maximum': 50, 'minimum': 1}, 'entity': {'type': 'string'}}}
find_relations
Find pathway 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.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'properties': {'limit': {'type': 'integer', 'default': 20, 'maximum': 50, 'minimum': 1}, 'effect': {'enum': ['activates', 'inhibits', 'binds', 'recruits', 'required-for', 'context-dependent', 'no-effect'], 'type': 'string'}, 'entity': {'type': 'string', 'description': 'Entity on either end of the relation'}, 'offset': {'type': 'integer', 'default': 0, 'maximum': 9007199254740991, 'minimum': 0, 'description': 'For the next page: pass next_offset from the previous answer.'}, 'source': {'type': 'string'}, 'target': {'type': 'string'}, 'contested_only': {'type': 'boolean', 'description': 'Only relations marked contested or with conflicting studies'}, 'strongest_at_least': {'enum': ['S', 'H', 'A', 'M', 'R', 'PP', 'RT'], 'type': 'string', 'description': 'Keep relations whose best supporting study is at least this code in the order S > H > A > M'}}}
get_entity
Get one entity
One entity (gene/protein, complex, drug, disease, process...) with its linked studies as short cards (first studies_limit) and every pathway relation it takes part in as a one-line claim. Accepts an id, a name or a synonym.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'required': ['entity'], 'properties': {'entity': {'type': 'string', 'description': 'e.g. "mTORC1", "Rheb", "rapamycin"'}, 'studies_limit': {'type': 'integer', 'default': 25, 'maximum': 50, 'minimum': 0}}}
get_question
Get one 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.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'required': ['id'], 'properties': {'id': {'type': 'string'}}}
get_relation
Get one relation
One pathway relation by ID (e.g. "RHEB-MTORC1"): mechanism, boundary conditions, confidence, supporting and conflicting studies.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'required': ['id'], 'properties': {'id': {'type': 'string'}}}
get_study
Get one study
Full record for one study by Atlas ID (e.g. "SAB1994"): abstract excerpt, extracted findings, linked entities, the relations it supports or contradicts, related open questions.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'required': ['sid'], 'properties': {'sid': {'type': 'string', 'description': 'Atlas study ID, e.g. "SAB1994"'}}}
list_questions
List open questions
The Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'properties': {'kind': {'enum': ['open-question', 'frontier'], 'type': 'string'}}}
search_entities
Search entities
Find genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'required': ['query'], 'properties': {'type': {'type': 'string', 'description': 'Optional type filter, e.g. "Drug", "Gene/Protein", "Disease"'}, 'limit': {'type': 'integer', 'default': 20, 'maximum': 100, 'minimum': 1}, 'query': {'type': 'string', 'description': 'Name or synonym, e.g. "raptor", "sirolimus"'}}}
search_studies
Search studies
Search the curated studies by keywords (title, finding, authors, journal, model system), optionally filtered by evidence code, a linked entity (gene, drug, disease...) and year range. Returns summary records with evidence codes and URLs.
読み取り専用 冪等
入力スキーマ 
{'type': 'object', '$schema': 'http://json-schema.org/draft-07/schema#', 'properties': {'limit': {'type': 'integer', 'default': 20, 'maximum': 50, 'minimum': 1}, 'query': {'type': 'string', 'description': 'Keywords, e.g. "rapamycin lifespan mice". Omit to list by filters only.'}, 'entity': {'type': 'string', 'description': 'Only studies linked to this entity (name, synonym or id), e.g. "Rheb".'}, 'offset': {'type': 'integer', 'default': 0, 'maximum': 9007199254740991, 'minimum': 0, 'description': 'For the next page: pass next_offset from the previous answer.'}, 'year_to': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991}, 'year_from': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991}, 'evidence_code': {'type': 'array', 'items': {'enum': ['S', 'H', 'A', 'M', 'R', 'PP', 'RT'], 'type': 'string'}, 'description': 'Keep only these evidence codes, e.g. ["H","S"] for human evidence.'}}}
履歴

最近のツール変更

追加
get_question
2026年10月2日2:40
追加
list_questions
2026年10月2日2:40
追加
find_contradictions
2026年10月2日2:40
追加
evidence_between
2026年10月2日2:40
追加
get_relation
2026年10月2日2:40
追加
find_relations
2026年10月2日2:40
追加
get_entity
2026年10月2日2:40
追加
search_entities
2026年10月2日2:40
追加
get_study
2026年10月2日2:40
追加
search_studies
2026年10月2日2:40
追加
atlas_about
2026年10月2日2:40
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