Forge Tools encode_screen_ccres

encode_screen_ccres read

scidex.forge.encode_screen_ccres

Query ENCODE SCREEN for classified cis-regulatory elements (cCREs). Returns promoter-like (PLS), proximal/distal enhancer-like (pELS/dELS), CTCF-only, and DNase-H3K4me3 elements with H3K4me3, H3K27ac, DNase, and CTCF signal Z-scores, plus nearest protein-coding gene. Covers 1M+ GRCh38 loci. Input: gene symbol (e.g. BRCA1) or genomic region (chr17:start-end). Distinct from forge_encode_epigenomics (raw ENCODE datasets) and forge_ensembl_regulatory (Ensembl Regulatory Build activity states).

HTTP: POST /api/scidex/forge/encode_screen_ccres

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.encode_screen_ccres``.",
  "properties": {
    "gene": {
      "anyOf": [
        {
          "maxLength": 50,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Gene symbol (e.g. ``BRCA1``, ``TP53``). Returns cCREs near the gene's TSS. At least one of ``gene`` or ``region`` is required.",
      "title": "Gene"
    },
    "region": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Genomic region in ``chr:start-end`` format (e.g. ``chr17:43044295-43125484``). Returns cCREs overlapping the region. At least one of ``gene`` or ``region`` is required.",
      "title": "Region"
    },
    "assembly": {
      "default": "GRCh38",
      "description": "Genome assembly (default ``GRCh38``; ``mm10`` is also supported by SCREEN).",
      "maxLength": 20,
      "title": "Assembly",
      "type": "string"
    },
    "element_type": {
      "anyOf": [
        {
          "maxLength": 20,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Filter by cCRE classification: ``PLS`` (promoter-like), ``pELS`` (proximal enhancer-like), ``dELS`` (distal enhancer-like), ``CTCF-only``, ``DNase-H3K4me3``. If ``None``, all classes are returned.",
      "title": "Element Type"
    },
    "biosample": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Biosample name (e.g. ``K562``, ``GM12878``) for tissue-specific Z-score context. Optional; if omitted, genome-wide maxZ scores are used.",
      "title": "Biosample"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of cCREs to return (1–500, default 20).",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeScreenIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "CcreElement": {
      "description": "One cCRE (cis-regulatory element) in the ENCODE SCREEN response.",
      "properties": {
        "accession": {
          "description": "ENCODE SCREEN accession (e.g. ``EH38E1516968``).",
          "title": "Accession",
          "type": "string"
        },
        "chrom": {
          "description": "Chromosome (e.g. ``chr17``).",
          "title": "Chrom",
          "type": "string"
        },
        "start": {
          "description": "Genomic start coordinate (0-based).",
          "title": "Start",
          "type": "integer"
        },
        "end": {
          "description": "Genomic end coordinate (exclusive).",
          "title": "End",
          "type": "integer"
        },
        "element_type": {
          "description": "cCRE classification: ``PLS`` (promoter-like), ``pELS`` (proximal enhancer-like), ``dELS`` (distal enhancer-like), ``CTCF-only``, or ``DNase-H3K4me3``.",
          "title": "Element Type",
          "type": "string"
        },
        "dnase_zscore": {
          "description": "DNase-seq signal Z-score.",
          "title": "Dnase Zscore",
          "type": "number"
        },
        "h3k4me3_zscore": {
          "description": "H3K4me3 ChIP-seq signal Z-score.",
          "title": "H3K4Me3 Zscore",
          "type": "number"
        },
        "h3k27ac_zscore": {
          "description": "H3K27ac ChIP-seq signal Z-score.",
          "title": "H3K27Ac Zscore",
          "type": "number"
        },
        "ctcf_zscore": {
          "description": "CTCF ChIP-seq signal Z-score.",
          "title": "Ctcf Zscore",
          "type": "number"
        },
        "nearest_gene": {
          "description": "Nearest protein-coding gene symbol.",
          "title": "Nearest Gene",
          "type": "string"
        },
        "nearest_gene_distance": {
          "description": "Distance (bp) to the nearest protein-coding gene's TSS; 0 if the cCRE overlaps the TSS.",
          "title": "Nearest Gene Distance",
          "type": "integer"
        }
      },
      "required": [
        "accession",
        "chrom",
        "start",
        "end",
        "element_type",
        "dnase_zscore",
        "h3k4me3_zscore",
        "h3k27ac_zscore",
        "ctcf_zscore",
        "nearest_gene",
        "nearest_gene_distance"
      ],
      "title": "CcreElement",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.encode_screen_ccres``.",
  "properties": {
    "elements": {
      "description": "Matching cCREs, capped at ``limit``.",
      "items": {
        "$ref": "#/$defs/CcreElement"
      },
      "title": "Elements",
      "type": "array"
    },
    "total_count": {
      "default": 0,
      "description": "Total cCREs matching the query (may exceed ``len(elements)`` when result count is larger than ``limit``).",
      "title": "Total Count",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream SCREEN API call (ms).",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeScreenOut",
  "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/encode_screen_ccres' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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