Forge Tools mondo_disease

mondo_disease read

scidex.forge.mondo_disease

Query the MONDO Integrated Disease Ontology via EBI OLS4 for harmonized disease identifiers that cross-map OMIM, Orphanet, DOID, MeSH, ICD, and NCIt into a single ontology with 10,000+ disease terms. Returns MONDO IDs, labels, definitions, synonyms, and cross-reference mappings grouped by vocabulary (OMIM, Orphanet, DOID, ICD10, MeSH). Used by Monarch Initiative, OpenTargets, and Alliance Genome as the canonical disease cross-mapping layer. Supports label search, exact MONDO ID lookup, and xref search. API: EBI OLS4 (ebi.ac.uk/ols4) — public, no authentication required.

HTTP: POST /api/scidex/forge/mondo_disease

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.mondo_disease``.",
  "properties": {
    "query": {
      "description": "Disease name, keyword, MONDO ID, or cross-reference identifier to search. Examples: 'type 2 diabetes', 'MONDO:0005148', 'OMIM:222100'.",
      "maxLength": 200,
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "default": "label",
      "description": "How to interpret ``query``. 'label' — free-text search across labels and synonyms (default). 'mondo_id' — exact match by MONDO identifier (e.g. 'MONDO:0005148'). 'xref' — search by cross-reference value (e.g. 'OMIM:222100').",
      "title": "Query Type",
      "type": "string"
    },
    "include_obsolete": {
      "default": false,
      "description": "When False (default), obsolete terms are excluded from results.",
      "title": "Include Obsolete",
      "type": "boolean"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of MONDO terms to return. Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeMondoDiseaseIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "MondoDiseaseTerm": {
      "description": "One MONDO disease ontology term.",
      "properties": {
        "mondo_id": {
          "description": "MONDO identifier, e.g. 'MONDO:0005148'.",
          "title": "Mondo Id",
          "type": "string"
        },
        "label": {
          "default": "",
          "description": "Preferred term label.",
          "title": "Label",
          "type": "string"
        },
        "definition": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Term definition text.",
          "title": "Definition"
        },
        "synonyms": {
          "description": "Exact and related synonyms from MONDO.",
          "items": {
            "type": "string"
          },
          "title": "Synonyms",
          "type": "array"
        },
        "xrefs": {
          "additionalProperties": {
            "items": {
              "type": "string"
            },
            "type": "array"
          },
          "description": "Cross-references grouped by vocabulary prefix. e.g. {'OMIM': ['222100'], 'Orphanet': ['65'], 'DOID': ['9352']}.",
          "title": "Xrefs",
          "type": "object"
        },
        "subclass_of": {
          "description": "Direct parent MONDO IDs (is_a hierarchy).",
          "items": {
            "type": "string"
          },
          "title": "Subclass Of",
          "type": "array"
        },
        "is_obsolete": {
          "default": false,
          "description": "True if this term has been deprecated in MONDO.",
          "title": "Is Obsolete",
          "type": "boolean"
        }
      },
      "required": [
        "mondo_id"
      ],
      "title": "MondoDiseaseTerm",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.mondo_disease``.",
  "properties": {
    "query": {
      "description": "The original query string.",
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "description": "The query mode used.",
      "title": "Query Type",
      "type": "string"
    },
    "terms": {
      "description": "MONDO disease terms matching the query.",
      "items": {
        "$ref": "#/$defs/MondoDiseaseTerm"
      },
      "title": "Terms",
      "type": "array"
    },
    "not_found": {
      "description": "True if no terms were found for the query.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "query",
    "query_type",
    "not_found"
  ],
  "title": "ForgeMondoDiseaseOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/mondo_disease' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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