Forge Tools panelapp_panels

panelapp_panels read

scidex.forge.panelapp_panels

Look up Genomics England PanelApp gene panels for a gene symbol. Returns curated diagnostic gene panels that include the queried gene, with confidence level (0–4; Green=3+), mode of inheritance (MOI), disease group, relevant disorders, and panel URLs. Free public API, no authentication required. REST API: https://panelapp.genomicsengland.co.uk/api/v1/

HTTP: POST /api/scidex/forge/panelapp_panels

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.panelapp_panels``.",
  "properties": {
    "gene_symbol": {
      "description": "HGNC gene symbol to query (e.g. ``'BRCA1'``, ``'CFTR'``). PanelApp returns all panels that include this gene.",
      "maxLength": 64,
      "title": "Gene Symbol",
      "type": "string"
    },
    "min_confidence": {
      "default": 0,
      "description": "Minimum confidence level to include (0 = all, 3 = Green only). Panels where the gene's confidence is below this threshold are excluded.",
      "maximum": 4,
      "minimum": 0,
      "title": "Min Confidence",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgePanelAppIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "PanelEntry": {
      "description": "One PanelApp gene-panel entry for a queried gene.",
      "properties": {
        "panel_id": {
          "description": "Numeric PanelApp panel ID.",
          "title": "Panel Id",
          "type": "integer"
        },
        "panel_name": {
          "description": "Panel display name.",
          "title": "Panel Name",
          "type": "string"
        },
        "panel_version": {
          "default": "",
          "description": "Panel version string (e.g. '4.27').",
          "title": "Panel Version",
          "type": "string"
        },
        "confidence_level": {
          "description": "Gene confidence level on this panel (0–4). Level 3 = Green (high evidence), 2 = Amber (moderate), 1 = Red (low).",
          "title": "Confidence Level",
          "type": "integer"
        },
        "confidence_label": {
          "default": "",
          "description": "Human-readable confidence label ('Green', 'Amber', 'Red', ...).",
          "title": "Confidence Label",
          "type": "string"
        },
        "mode_of_inheritance": {
          "default": "",
          "description": "Mode of inheritance annotation as recorded on the panel (e.g. 'MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted').",
          "title": "Mode Of Inheritance",
          "type": "string"
        },
        "disease_group": {
          "default": "",
          "description": "Top-level disease group for the panel.",
          "title": "Disease Group",
          "type": "string"
        },
        "disease_sub_group": {
          "default": "",
          "description": "Disease sub-group for the panel.",
          "title": "Disease Sub Group",
          "type": "string"
        },
        "relevant_disorders": {
          "description": "Relevant disorder names associated with the panel.",
          "items": {
            "type": "string"
          },
          "title": "Relevant Disorders",
          "type": "array"
        },
        "panel_url": {
          "default": "",
          "description": "Canonical PanelApp URL for the panel.",
          "title": "Panel Url",
          "type": "string"
        }
      },
      "required": [
        "panel_id",
        "panel_name",
        "confidence_level"
      ],
      "title": "PanelEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.panelapp_panels``.",
  "properties": {
    "gene_symbol": {
      "description": "The gene symbol that was queried.",
      "title": "Gene Symbol",
      "type": "string"
    },
    "panels": {
      "description": "PanelApp gene panels that contain this gene, ordered by descending confidence level then panel name.",
      "items": {
        "$ref": "#/$defs/PanelEntry"
      },
      "title": "Panels",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the gene was not found in any PanelApp panel.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "Genomics England PanelApp",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol",
    "took_ms"
  ],
  "title": "ForgePanelAppOut",
  "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/panelapp_panels' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

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