Forge Tools omim_disease

omim_disease read

scidex.forge.omim_disease

Query OMIM for Mendelian disease entries by gene symbol, MIM number, or phenotype name. Returns entries with causative genes, inheritance modes (AD/AR/XL), associated phenotype MIM numbers, and brief synopsis. OMIM is the authoritative Mendelian disease catalog — use this for structured inheritance-mode data unavailable from DisGeNET.

HTTP: POST /api/scidex/forge/omim_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.omim_disease``.",
  "properties": {
    "gene_symbol": {
      "anyOf": [
        {
          "maxLength": 30,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "HGNC gene symbol to look up (e.g. ``BRCA1``, ``HTT``, ``CFTR``). Returns all OMIM entries where this gene is a causative gene.",
      "title": "Gene Symbol"
    },
    "mim_number": {
      "anyOf": [
        {
          "maxLength": 20,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "OMIM MIM number string (e.g. ``113705`` for BRCA1 locus, ``604370`` for BRCA1-related breast cancer). Fetches the exact entry.",
      "title": "Mim Number"
    },
    "phenotype_query": {
      "anyOf": [
        {
          "maxLength": 200,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Free-text phenotype or disease name to search (e.g. ``'Huntington disease'``, ``'cystic fibrosis'``).",
      "title": "Phenotype Query"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of OMIM entries to return. Default 10.",
      "maximum": 50,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeOMIMIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "OMIMEntry": {
      "description": "One OMIM entry in the response.",
      "properties": {
        "mim_number": {
          "description": "OMIM MIM number (e.g. '113705' for BRCA1).",
          "title": "Mim Number",
          "type": "string"
        },
        "title": {
          "default": "",
          "description": "Preferred OMIM entry title.",
          "title": "Title",
          "type": "string"
        },
        "type": {
          "default": "other",
          "description": "Entry type: 'gene', 'phenotype', 'removed', or 'other'.",
          "title": "Type",
          "type": "string"
        },
        "gene_symbols": {
          "description": "HGNC gene symbols associated with this entry.",
          "items": {
            "type": "string"
          },
          "title": "Gene Symbols",
          "type": "array"
        },
        "inheritance_modes": {
          "description": "Normalized inheritance mode codes: AD (autosomal dominant), AR (autosomal recessive), XL (X-linked), YL (Y-linked), MT (mitochondrial), SM (somatic mutation).",
          "items": {
            "type": "string"
          },
          "title": "Inheritance Modes",
          "type": "array"
        },
        "phenotype_mim_numbers": {
          "description": "MIM numbers of associated phenotype entries.",
          "items": {
            "type": "string"
          },
          "title": "Phenotype Mim Numbers",
          "type": "array"
        },
        "synopsis_snippet": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "First 300 chars of the entry description, if available.",
          "title": "Synopsis Snippet"
        }
      },
      "required": [
        "mim_number"
      ],
      "title": "OMIMEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.omim_disease``.",
  "properties": {
    "entries": {
      "items": {
        "$ref": "#/$defs/OMIMEntry"
      },
      "title": "Entries",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total results reported by OMIM. May exceed len(entries) since OMIM returns up to ``limit`` entries per call.",
      "title": "Total Found",
      "type": "integer"
    },
    "returned": {
      "description": "Length of ``entries``.",
      "title": "Returned",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "returned",
    "took_ms"
  ],
  "title": "ForgeOMIMOut",
  "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/omim_disease' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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