Oliver's mTOR Atlas

Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset.

{
  "type": "object",
  "properties": {}
}

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.

{
  "type": "object",
  "properties": {
    "query": {
      "description": "Keywords, e.g. \"rapamycin lifespan mice\". Omit to list by filters only.",
      "type": "string"
    },
    "evidence_code": {
      "description": "Keep only these evidence codes, e.g. [\"H\",\"S\"] for human evidence.",
      "type": "array",
      "items": {
        "type": "string",
        "enum": [
          "S",
          "H",
          "A",
          "M",
          "R",
          "PP",
          "RT"
        ]
      }
    },
    "entity": {
      "description": "Only studies linked to this entity (name, synonym or id), e.g. \"Rheb\".",
      "type": "string"
    },
    "year_from": {
      "type": "integer",
      "minimum": -9007199254740991,
      "maximum": 9007199254740991
    },
    "year_to": {
      "type": "integer",
      "minimum": -9007199254740991,
      "maximum": 9007199254740991
    },
    "limit": {
      "default": 20,
      "type": "integer",
      "minimum": 1,
      "maximum": 50
    },
    "offset": {
      "default": 0,
      "description": "For the next page: pass next_offset from the previous answer.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    }
  },
  "$schema": "http://json-schema.org/draft-07/schema#"
}

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.

{
  "type": "object",
  "properties": {
    "sid": {
      "type": "string",
      "description": "Atlas study ID, e.g. \"SAB1994\""
    }
  },
  "required": [
    "sid"
  ],
  "$schema": "http://json-schema.org/draft-07/schema#"
}

Find genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym.

{
  "type": "object",
  "properties": {
    "query": {
      "type": "string",
      "description": "Name or synonym, e.g. \"raptor\", \"sirolimus\""
    },
    "type": {
      "description": "Optional type filter, e.g. \"Drug\", \"Gene/Protein\", \"Disease\"",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "type": "integer",
      "minimum": 1,
      "maximum": 100
    }
  },
  "required": [
    "query"
  ],
  "$schema": "http://json-schema.org/draft-07/schema#"
}

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.

{
  "type": "object",
  "properties": {
    "entity": {
      "type": "string",
      "description": "e.g. \"mTORC1\", \"Rheb\", \"rapamycin\""
    },
    "studies_limit": {
      "default": 25,
      "type": "integer",
      "minimum": 0,
      "maximum": 50
    }
  },
  "required": [
    "entity"
  ],
  "$schema": "http://json-schema.org/draft-07/schema#"
}

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.

{
  "type": "object",
  "properties": {
    "entity": {
      "description": "Entity on either end of the relation",
      "type": "string"
    },
    "source": {
      "type": "string"
    },
    "target": {
      "type": "string"
    },
    "effect": {
      "type": "string",
      "enum": [
        "activates",
        "inhibits",
        "binds",
        "recruits",
        "required-for",
        "context-dependent",
        "no-effect"
      ]
    },
    "contested_only": {
      "description": "Only relations marked contested or with conflicting studies",
      "type": "boolean"
    },
    "strongest_at_least": {
      "description": "Keep relations whose best supporting study is at least this code in the order S > H > A > M",
      "type": "string",
      "enum": [
        "S",
        "H",
        "A",
        "M",
        "R",
        "PP",
        "RT"
      ]
    },
    "limit": {
      "default": 20,
      "type": "integer",
      "minimum": 1,
      "maximum": 50
    },
    "offset": {
      "default": 0,
      "description": "For the next page: pass next_offset from the previous answer.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    }
  },
  "$schema": "http://json-schema.org/draft-07/schema#"
}

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

{
  "type": "object",
  "properties": {
    "id": {
      "type": "string"
    }
  },
  "required": [
    "id"
  ],
  "$schema": "http://json-schema.org/draft-07/schema#"
}

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?".

{
  "type": "object",
  "properties": {
    "a": {
      "type": "string"
    },
    "b": {
      "type": "string"
    }
  },
  "required": [
    "a",
    "b"
  ],
  "$schema": "http://json-schema.org/draft-07/schema#"
}

Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. Optionally limited to one entity.

{
  "type": "object",
  "properties": {
    "entity": {
      "type": "string"
    },
    "limit": {
      "default": 20,
      "type": "integer",
      "minimum": 1,
      "maximum": 50
    }
  },
  "$schema": "http://json-schema.org/draft-07/schema#"
}

The Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions.

{
  "type": "object",
  "properties": {
    "kind": {
      "type": "string",
      "enum": [
        "open-question",
        "frontier"
      ]
    }
  },
  "$schema": "http://json-schema.org/draft-07/schema#"
}

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.

{
  "type": "object",
  "properties": {
    "id": {
      "type": "string"
    }
  },
  "required": [
    "id"
  ],
  "$schema": "http://json-schema.org/draft-07/schema#"
}