Forge Tools orphanet_disease

orphanet_disease read

scidex.forge.orphanet_disease

Search Orphanet rare disease records via OLS4/ORDO. Returns disease entities with ORPHA codes, synonyms, prevalence class, inheritance modes, associated genes, and OMIM/ICD-10 cross-references.

HTTP: POST /api/scidex/forge/orphanet_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 
{
  "description": "Input schema for ``scidex.forge.orphanet_disease``.",
  "properties": {
    "query": {
      "description": "Disease name or keyword to search in Orphanet, e.g. ``cystic fibrosis``.",
      "maxLength": 200,
      "title": "Query",
      "type": "string"
    },
    "search_mode": {
      "default": "disease",
      "description": "Search mode — currently only ``'disease'`` is supported.",
      "title": "Search Mode",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of disease records to return. Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeOrphanetIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "OrphanetDisease": {
      "description": "One rare disease result from Orphanet.",
      "properties": {
        "orpha_code": {
          "description": "Orphanet accession, e.g. ``ORPHA:586``.",
          "title": "Orpha Code",
          "type": "string"
        },
        "disease_name": {
          "description": "Official disease name.",
          "title": "Disease Name",
          "type": "string"
        },
        "synonyms": {
          "description": "Alternative disease names.",
          "items": {
            "type": "string"
          },
          "title": "Synonyms",
          "type": "array"
        },
        "prevalence": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Prevalence class (absent if not annotated).",
          "title": "Prevalence"
        },
        "inheritance_modes": {
          "description": "Modes of inheritance.",
          "items": {
            "type": "string"
          },
          "title": "Inheritance Modes",
          "type": "array"
        },
        "associated_genes": {
          "description": "Gene symbols associated with this disease.",
          "items": {
            "type": "string"
          },
          "title": "Associated Genes",
          "type": "array"
        },
        "omim_ids": {
          "description": "OMIM cross-references.",
          "items": {
            "type": "string"
          },
          "title": "Omim Ids",
          "type": "array"
        },
        "icd10_codes": {
          "description": "ICD-10 cross-references.",
          "items": {
            "type": "string"
          },
          "title": "Icd10 Codes",
          "type": "array"
        },
        "ols_url": {
          "description": "OLS4 browser URL for this ORDO term.",
          "title": "Ols Url",
          "type": "string"
        }
      },
      "required": [
        "orpha_code",
        "disease_name",
        "ols_url"
      ],
      "title": "OrphanetDisease",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.orphanet_disease``.",
  "properties": {
    "query": {
      "description": "The query string that was searched.",
      "title": "Query",
      "type": "string"
    },
    "diseases": {
      "description": "Matching rare disease records.",
      "items": {
        "$ref": "#/$defs/OrphanetDisease"
      },
      "title": "Diseases",
      "type": "array"
    },
    "total_found": {
      "description": "Total results reported by OLS4 (may exceed ``diseases`` length).",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for all upstream calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query",
    "total_found",
    "took_ms"
  ],
  "title": "ForgeOrphanetOut",
  "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/orphanet_disease' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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