Forge Tools disease_ontology

disease_ontology read

scidex.forge.disease_ontology

Query the OBO Disease Ontology (DO) via EBI OLS4 for disease terms, hierarchy, synonyms, and clinical vocabulary cross-references (OMIM, ICD-9, ICD-10, MeSH). Given a disease name or DOID (e.g. DOID:9352 for type 2 diabetes mellitus), returns term hierarchy, cross-references, synonyms, definition, and obsolescence status. Bridges clinical vocabularies — maps disease names to OMIM/ICD/MeSH codes. Complements scidex.forge.hpo_phenotype (phenotype terms) and scidex.forge.omim_disease (Mendelian disease entries). API: EBI OLS4 (ebi.ac.uk/ols4) — public, no authentication required.

HTTP: POST /api/scidex/forge/disease_ontology

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.disease_ontology``.",
  "properties": {
    "query": {
      "description": "Disease name or keyword to search (e.g. 'lung cancer', 'diabetes mellitus', 'asthma'). Used as the free-text search when ``doid`` is not provided.",
      "maxLength": 200,
      "title": "Query",
      "type": "string"
    },
    "doid": {
      "anyOf": [
        {
          "maxLength": 20,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional DOID identifier for direct/exact term lookup (e.g. 'DOID:9352' for type 2 diabetes mellitus). When provided, performs an exact search by DOID instead of free-text.",
      "title": "Doid"
    },
    "limit": {
      "default": 5,
      "description": "Maximum number of Disease Ontology terms to return. Default 5.",
      "maximum": 50,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeDiseaseOntologyIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "DiseaseOntologyEntry": {
      "description": "One Disease Ontology term in the response.",
      "properties": {
        "doid": {
          "description": "DOID identifier (e.g. 'DOID:9352').",
          "title": "Doid",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Term label/name.",
          "title": "Name",
          "type": "string"
        },
        "definition": {
          "default": "",
          "description": "Term definition (may be empty).",
          "title": "Definition",
          "type": "string"
        },
        "synonyms": {
          "description": "Synonym terms from the Disease Ontology.",
          "items": {
            "type": "string"
          },
          "title": "Synonyms",
          "type": "array"
        },
        "xrefs": {
          "description": "Cross-references to clinical vocabularies: OMIM, ICD9CM, ICD10CM, MeSH, NCI, SNOMEDCT_US, etc.",
          "items": {
            "type": "string"
          },
          "title": "Xrefs",
          "type": "array"
        },
        "parent_terms": {
          "description": "Direct parent DOID term IDs (is_a hierarchy).",
          "items": {
            "type": "string"
          },
          "title": "Parent Terms",
          "type": "array"
        },
        "is_obsolete": {
          "default": false,
          "description": "True if this term has been deprecated in the Disease Ontology.",
          "title": "Is Obsolete",
          "type": "boolean"
        }
      },
      "required": [
        "doid"
      ],
      "title": "DiseaseOntologyEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.disease_ontology``.",
  "properties": {
    "results": {
      "description": "Disease Ontology terms matching the query.",
      "items": {
        "$ref": "#/$defs/DiseaseOntologyEntry"
      },
      "title": "Results",
      "type": "array"
    },
    "total_found": {
      "description": "Number of terms returned.",
      "title": "Total Found",
      "type": "integer"
    },
    "not_found": {
      "description": "True if no Disease Ontology terms were found for the query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "Disease Ontology via EBI OLS4 (ebi.ac.uk/ols4)",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "total_found",
    "not_found"
  ],
  "title": "ForgeDiseaseOntologyOut",
  "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/disease_ontology' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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