Server definition

Hash: sha256:c933447ecc2c98d94d6eae8c920fdad702d6a5322486228931bc12af187d35ed
What it is: What a remote MCP server returned when asked what it offers: 11 tools

The blob, as servednamed by its sha256

{
  "instructions": "Oliver's mTOR Atlas is a curated, evidence-labelled corpus of mTOR research (studies, entities, signed pathway relations, open questions).\nHow to use it well:\n- Every study has an evidence code: S synthesis of human data, H human study, A animal model, M molecular/in vitro, R review, PP preprint, RT registered trial. The code describes the KIND of study, not its quality. Do not present an M finding as if it were shown in people.\n- A relation is a claim (source -> effect -> target) with supporting and conflicting studies, boundary conditions, a consensus flag and a human-relevance grade. Quote the boundary when you use a relation.\n- \"Not in the Atlas\" means not in this curated corpus, not \"not known\". Say so.\n- Cite the study or relation 'url' fields, and the dataset (doi:10.5281/zenodo.22059963) with the dataset_version and corpus_snapshot from atlas_about.",
  "tools": [
    {
      "description": "Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset.",
      "inputSchema": {
        "properties": {},
        "type": "object"
      },
      "name": "atlas_about",
      "outputSchema": null
    },
    {
      "description": "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?\".",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "a": {
            "type": "string"
          },
          "b": {
            "type": "string"
          }
        },
        "required": [
          "a",
          "b"
        ],
        "type": "object"
      },
      "name": "evidence_between",
      "outputSchema": null
    },
    {
      "description": "Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. Optionally limited to one entity.",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "entity": {
            "type": "string"
          },
          "limit": {
            "default": 20,
            "maximum": 50,
            "minimum": 1,
            "type": "integer"
          }
        },
        "type": "object"
      },
      "name": "find_contradictions",
      "outputSchema": null
    },
    {
      "description": "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.",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "contested_only": {
            "description": "Only relations marked contested or with conflicting studies",
            "type": "boolean"
          },
          "effect": {
            "enum": [
              "activates",
              "inhibits",
              "binds",
              "recruits",
              "required-for",
              "context-dependent",
              "no-effect"
            ],
            "type": "string"
          },
          "entity": {
            "description": "Entity on either end of the relation",
            "type": "string"
          },
          "limit": {
            "default": 20,
            "maximum": 50,
            "minimum": 1,
            "type": "integer"
          },
          "offset": {
            "default": 0,
            "description": "For the next page: pass next_offset from the previous answer.",
            "maximum": 9007199254740991,
            "minimum": 0,
            "type": "integer"
          },
          "source": {
            "type": "string"
          },
          "strongest_at_least": {
            "description": "Keep relations whose best supporting study is at least this code in the order S > H > A > M",
            "enum": [
              "S",
              "H",
              "A",
              "M",
              "R",
              "PP",
              "RT"
            ],
            "type": "string"
          },
          "target": {
            "type": "string"
          }
        },
        "type": "object"
      },
      "name": "find_relations",
      "outputSchema": null
    },
    {
      "description": "One entity (gene/protein, complex, drug, disease, process...) with its linked studies as short cards (first studies_limit) and every pathway relation it takes part in as a one-line claim. Accepts an id, a name or a synonym.",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "entity": {
            "description": "e.g. \"mTORC1\", \"Rheb\", \"rapamycin\"",
            "type": "string"
          },
          "studies_limit": {
            "default": 25,
            "maximum": 50,
            "minimum": 0,
            "type": "integer"
          }
        },
        "required": [
          "entity"
        ],
        "type": "object"
      },
      "name": "get_entity",
      "outputSchema": null
    },
    {
      "description": "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.",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "id": {
            "type": "string"
          }
        },
        "required": [
          "id"
        ],
        "type": "object"
      },
      "name": "get_question",
      "outputSchema": null
    },
    {
      "description": "One pathway relation by ID (e.g. \"RHEB-MTORC1\"): mechanism, boundary conditions, confidence, supporting and conflicting studies.",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "id": {
            "type": "string"
          }
        },
        "required": [
          "id"
        ],
        "type": "object"
      },
      "name": "get_relation",
      "outputSchema": null
    },
    {
      "description": "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.",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "sid": {
            "description": "Atlas study ID, e.g. \"SAB1994\"",
            "type": "string"
          }
        },
        "required": [
          "sid"
        ],
        "type": "object"
      },
      "name": "get_study",
      "outputSchema": null
    },
    {
      "description": "The Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions.",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "kind": {
            "enum": [
              "open-question",
              "frontier"
            ],
            "type": "string"
          }
        },
        "type": "object"
      },
      "name": "list_questions",
      "outputSchema": null
    },
    {
      "description": "Find genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym.",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "limit": {
            "default": 20,
            "maximum": 100,
            "minimum": 1,
            "type": "integer"
          },
          "query": {
            "description": "Name or synonym, e.g. \"raptor\", \"sirolimus\"",
            "type": "string"
          },
          "type": {
            "description": "Optional type filter, e.g. \"Drug\", \"Gene/Protein\", \"Disease\"",
            "type": "string"
          }
        },
        "required": [
          "query"
        ],
        "type": "object"
      },
      "name": "search_entities",
      "outputSchema": null
    },
    {
      "description": "Search the curated studies by keywords (title, finding, authors, journal, model system), optionally filtered by evidence code, a linked entity (gene, drug, disease...) and year range. Returns summary records with evidence codes and URLs.",
      "inputSchema": {
        "$schema": "http://json-schema.org/draft-07/schema#",
        "properties": {
          "entity": {
            "description": "Only studies linked to this entity (name, synonym or id), e.g. \"Rheb\".",
            "type": "string"
          },
          "evidence_code": {
            "description": "Keep only these evidence codes, e.g. [\"H\",\"S\"] for human evidence.",
            "items": {
              "enum": [
                "S",
                "H",
                "A",
                "M",
                "R",
                "PP",
                "RT"
              ],
              "type": "string"
            },
            "type": "array"
          },
          "limit": {
            "default": 20,
            "maximum": 50,
            "minimum": 1,
            "type": "integer"
          },
          "offset": {
            "default": 0,
            "description": "For the next page: pass next_offset from the previous answer.",
            "maximum": 9007199254740991,
            "minimum": 0,
            "type": "integer"
          },
          "query": {
            "description": "Keywords, e.g. \"rapamycin lifespan mice\". Omit to list by filters only.",
            "type": "string"
          },
          "year_from": {
            "maximum": 9007199254740991,
            "minimum": -9007199254740991,
            "type": "integer"
          },
          "year_to": {
            "maximum": 9007199254740991,
            "minimum": -9007199254740991,
            "type": "integer"
          }
        },
        "type": "object"
      },
      "name": "search_studies",
      "outputSchema": null
    }
  ]
}

Verify it yourself

curl -s https://api.teppi.xyz/v1/evidence/sha256:c933447ecc2c98d94d6eae8c920fdad702d6a5322486228931bc12af187d35ed | sha256sum