Forge Tools depmap_gene_effect

depmap_gene_effect read

scidex.forge.depmap_gene_effect

Return CRISPR Cas9 gene effect scores from the Broad Institute DepMap portal for a given gene across cancer cell lines. Score near 0 = non-essential; score ≤ -0.5 = essential (cell dies on KO). Returns per-cell-line effect_score and z_score, ranked by strongest dependency, plus summary stats: mean_effect_score, essential_cell_lines count, not_essential_cell_lines count. Optional lineage_filter restricts results to one cancer lineage. API: https://depmap.org/portal/api — free, no auth required.

HTTP: POST /api/scidex/forge/depmap_gene_effect

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.depmap_gene_effect``.",
  "properties": {
    "gene_symbol": {
      "description": "HGNC gene symbol to query (e.g. ``'TP53'``, ``'BRCA1'``, ``'EGFR'``). Case-insensitive; normalised to upper-case before the API call.",
      "maxLength": 64,
      "title": "Gene Symbol",
      "type": "string"
    },
    "top_n_cell_lines": {
      "default": 10,
      "description": "Number of cell lines to return, ranked by most-negative effect score (strongest dependency first). Default 10, max 200.",
      "maximum": 200,
      "minimum": 1,
      "title": "Top N Cell Lines",
      "type": "integer"
    },
    "lineage_filter": {
      "default": "",
      "description": "Restrict results to a single cancer lineage (e.g. ``'lung'``, ``'breast'``, ``'haematopoietic_and_lymphoid'``). Case-insensitive substring match against the lineage field. Empty string (default) returns all lineages.",
      "maxLength": 128,
      "title": "Lineage Filter",
      "type": "string"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeDepMapIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "DepMapEffectScore": {
      "description": "Per-cell-line CRISPR gene effect score from DepMap.",
      "properties": {
        "cell_line_name": {
          "description": "Cell line display name (e.g. 'A549').",
          "title": "Cell Line Name",
          "type": "string"
        },
        "cell_line_id": {
          "default": "",
          "description": "DepMap cell line ID (e.g. 'ACH-000001').",
          "title": "Cell Line Id",
          "type": "string"
        },
        "lineage": {
          "description": "Cancer lineage (e.g. 'lung', 'breast').",
          "title": "Lineage",
          "type": "string"
        },
        "effect_score": {
          "description": "CRISPR gene effect score. Near 0 = non-essential; ≤ -0.5 = essential (cell dies on KO).",
          "title": "Effect Score",
          "type": "number"
        },
        "z_score": {
          "description": "Z-normalised effect score across all returned cell lines.",
          "title": "Z Score",
          "type": "number"
        }
      },
      "required": [
        "cell_line_name",
        "lineage",
        "effect_score",
        "z_score"
      ],
      "title": "DepMapEffectScore",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.depmap_gene_effect``.",
  "properties": {
    "gene_symbol": {
      "description": "The gene symbol queried (upper-case).",
      "title": "Gene Symbol",
      "type": "string"
    },
    "effect_scores": {
      "description": "Per-cell-line CRISPR effect scores, ranked by most-negative score (strongest dependency first), up to ``top_n_cell_lines``.",
      "items": {
        "$ref": "#/$defs/DepMapEffectScore"
      },
      "title": "Effect Scores",
      "type": "array"
    },
    "mean_effect_score": {
      "anyOf": [
        {
          "type": "number"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Arithmetic mean gene effect score across all returned cell lines.",
      "title": "Mean Effect Score"
    },
    "essential_cell_lines": {
      "default": 0,
      "description": "Count of returned cell lines with effect_score ≤ -0.5.",
      "title": "Essential Cell Lines",
      "type": "integer"
    },
    "not_essential_cell_lines": {
      "default": 0,
      "description": "Count of returned cell lines with effect_score > -0.5.",
      "title": "Not Essential Cell Lines",
      "type": "integer"
    },
    "total_cell_lines_queried": {
      "default": 0,
      "description": "Total cell lines in the DepMap response before filtering/truncation.",
      "title": "Total Cell Lines Queried",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol",
    "took_ms"
  ],
  "title": "ForgeDepMapOut",
  "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/depmap_gene_effect' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

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