Forge Tools gene2phenotype_g2p

gene2phenotype_g2p read

scidex.forge.gene2phenotype_g2p

Query the EBI Gene2Phenotype (DDG2P) database for curated gene-disease associations across developmental disorders, cancer, and malformations panels. For a gene symbol, returns disease names, allelic requirements (biallelic / monoallelic), confidence levels (confirmed / probable / possible), HPO terms, and PubMed IDs. Source: https://www.ebi.ac.uk/gene2phenotype/ — public, no auth required.

HTTP: POST /api/scidex/forge/gene2phenotype_g2p

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.gene2phenotype_g2p``.",
  "properties": {
    "gene_symbol": {
      "description": "HGNC gene symbol to query (e.g. ``'BRCA1'``, ``'SCN1A'``). One gene per call.",
      "maxLength": 30,
      "minLength": 1,
      "title": "Gene Symbol",
      "type": "string"
    },
    "panel": {
      "anyOf": [
        {
          "maxLength": 50,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional G2P panel to filter by. Accepted values: ``'DDG2P'`` (developmental disorders), ``'cancer'``, ``'malformations'``, ``'intellectual disability'``, ``'epilepsy'``, ``'skeletal'``, ``'skin'``, ``'cardiac'``, ``'renal'``, ``'respiratory'``. If None, searches all panels.",
      "title": "Panel"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of G2P records to return. Default 50.",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeG2PIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "G2PAssociation": {
      "description": "One G2P gene-disease association in the response.",
      "properties": {
        "disease_name": {
          "description": "Disease name (G2P canonical).",
          "title": "Disease Name",
          "type": "string"
        },
        "disease_id": {
          "description": "G2P internal disease identifier.",
          "title": "Disease Id",
          "type": "string"
        },
        "panel": {
          "description": "G2P panel this record belongs to.",
          "title": "Panel",
          "type": "string"
        },
        "allelic_requirement": {
          "default": "",
          "description": "allelic requirement: 'biallelic', 'monoallelic', 'both biallelic and monoallelic', 'unknown', 'not specified', 'miRNA target'.",
          "title": "Allelic Requirement",
          "type": "string"
        },
        "confidence": {
          "default": "",
          "description": "G2P confidence: 'confirmed', 'probable', 'possible', 'case-only', 'child of confirmed'.",
          "title": "Confidence",
          "type": "string"
        },
        "cross_cutting_modifier": {
          "default": "",
          "description": "Cross-cutting modifier if any.",
          "title": "Cross Cutting Modifier",
          "type": "string"
        },
        "organ_specificity": {
          "default": "",
          "description": "Organ or tissue specificity.",
          "title": "Organ Specificity",
          "type": "string"
        },
        "hpo_id": {
          "default": "",
          "description": "HPO term ID, if any (e.g. 'HP:0001234').",
          "title": "Hpo Id",
          "type": "string"
        },
        "hpo_term": {
          "default": "",
          "description": "HPO term name, if any.",
          "title": "Hpo Term",
          "type": "string"
        },
        "pmids": {
          "description": "PubMed IDs supporting this association.",
          "items": {
            "type": "string"
          },
          "title": "Pmids",
          "type": "array"
        }
      },
      "required": [
        "disease_name",
        "disease_id",
        "panel"
      ],
      "title": "G2PAssociation",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.gene2phenotype_g2p``.",
  "properties": {
    "gene_symbol": {
      "description": "Queried gene symbol (as supplied).",
      "title": "Gene Symbol",
      "type": "string"
    },
    "records": {
      "description": "G2P gene-disease association records.",
      "items": {
        "$ref": "#/$defs/G2PAssociation"
      },
      "title": "Records",
      "type": "array"
    },
    "returned": {
      "description": "Length of ``records``.",
      "title": "Returned",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True when G2P returned no records for this gene.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "Gene2Phenotype (DDG2P)",
      "description": "Data source: 'Gene2Phenotype (DDG2P)'.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream G2P call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol",
    "returned",
    "took_ms"
  ],
  "title": "ForgeG2POut",
  "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/gene2phenotype_g2p' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

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