Forge Tools chip_atlas

chip_atlas read

scidex.forge.chip_atlas

Query ChIP-Atlas (chip-atlas.org) for TF/histone binding experiments near a gene or in a genomic region. ChIP-Atlas aggregates all public ChIP-seq experiments from NCBI SRA, providing peak-call tracks for thousands of TFs and histone marks across hundreds of cell types. Distinct from GTRD (merged consensus) and ENCODE ChIP-seq (single portal): ChIP-Atlas covers the full public SRA catalogue with uniform processing. Query by gene symbol, antigen (TF/histone), and/or genomic region. Returns experiment accession (SRX), antigen, cell type, peak count, and direct ChIP-Atlas URL. Not-found queries return not_found=True. API: chip-atlas.dbcls.jp — public, no auth required.

HTTP: POST /api/scidex/forge/chip_atlas

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.chip_atlas``.",
  "properties": {
    "gene_symbol": {
      "anyOf": [
        {
          "maxLength": 64,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "HGNC gene symbol to query for binding events near its TSS (e.g. ``'TP53'``, ``'MYC'``, ``'CTCF'``). At least one of ``gene_symbol``, ``antigen``, or ``region`` is required.",
      "title": "Gene Symbol"
    },
    "antigen": {
      "anyOf": [
        {
          "maxLength": 64,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "TF or histone modification name to filter experiments (e.g. ``'CTCF'``, ``'H3K27ac'``, ``'H3K4me3'``). At least one of ``gene_symbol``, ``antigen``, or ``region`` is required.",
      "title": "Antigen"
    },
    "region": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Genomic region in ``chr:start-end`` format to search for peaks (e.g. ``'chr17:7676000-7680000'``). At least one of ``gene_symbol``, ``antigen``, or ``region`` is required.",
      "title": "Region"
    },
    "genome": {
      "default": "hg38",
      "description": "Reference genome assembly (default ``'hg38'``). Also supported: ``'mm10'``, ``'rn6'``, ``'dm6'``, ``'ce11'``, ``'sacCer3'``.",
      "maxLength": 20,
      "title": "Genome",
      "type": "string"
    },
    "cell_type": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Cell type or tissue filter (e.g. ``'K562'``, ``'liver'``).",
      "title": "Cell Type"
    },
    "threshold": {
      "default": 200,
      "description": "Peak height threshold for filtering experiments (default 200). Higher values return only the strongest binding events.",
      "maximum": 10000,
      "minimum": 10,
      "title": "Threshold",
      "type": "integer"
    },
    "distance": {
      "default": 1000,
      "description": "Distance from gene TSS in bp to count binding peaks (default 1000). Larger values capture distal regulatory elements.",
      "maximum": 100000,
      "minimum": 100,
      "title": "Distance",
      "type": "integer"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of results to return (default 20).",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeChIPAtlasIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ChIPAtlasResult": {
      "description": "One ChIP-Atlas binding experiment result.",
      "properties": {
        "srx_id": {
          "description": "SRA experiment accession (e.g. 'SRX123456').",
          "title": "Srx Id",
          "type": "string"
        },
        "antigen": {
          "default": "",
          "description": "TF or histone modification (e.g. 'CTCF').",
          "title": "Antigen",
          "type": "string"
        },
        "cell_type": {
          "default": "",
          "description": "Cell line or tissue name (e.g. 'K562').",
          "title": "Cell Type",
          "type": "string"
        },
        "peak_count": {
          "default": 0,
          "description": "Number of peaks near the queried gene in this experiment.",
          "minimum": 0,
          "title": "Peak Count",
          "type": "integer"
        },
        "title": {
          "default": "",
          "description": "Experiment title from ChIP-Atlas metadata.",
          "title": "Title",
          "type": "string"
        },
        "chip_url": {
          "default": "",
          "description": "Direct ChIP-Atlas experiment link.",
          "title": "Chip Url",
          "type": "string"
        }
      },
      "required": [
        "srx_id"
      ],
      "title": "ChIPAtlasResult",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.chip_atlas``.",
  "properties": {
    "query": {
      "description": "Human-readable description of the query submitted.",
      "title": "Query",
      "type": "string"
    },
    "results": {
      "description": "ChIP-Atlas binding experiment results matching the query.",
      "items": {
        "$ref": "#/$defs/ChIPAtlasResult"
      },
      "title": "Results",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no binding experiments were found for the query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "ChIP-Atlas (chip-atlas.org)",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeChIPAtlasOut",
  "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/chip_atlas' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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