remap_tfbs read

{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.remap_tfbs``.",
  "properties": {
    "tf_symbol": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Transcription factor gene symbol to query (e.g. 'FOXA1', 'CTCF'). Either ``tf_symbol`` or ``region`` must be provided, but not both. Case-insensitive; will be uppercased for the API call.",
      "title": "Tf Symbol"
    },
    "region": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Genomic region in ``chr:start-end`` format (e.g. ``'chr8:127000000-127001000'``). Either ``tf_symbol`` or ``region`` must be provided, but not both. 1-based coordinates are converted to 0-based internally.",
      "title": "Region"
    },
    "genome": {
      "default": "hg38",
      "description": "Reference genome assembly. Default ``'hg38'`` (Homo sapiens). Also accepts ``'hg19'``, ``'mm10'``, ``'mm39'``, ``'dm6'`` (Drosophila), ``'at'`` (Arabidopsis).",
      "title": "Genome",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of peak records to return. Default 20.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeRemapTfbsIn",
  "type": "object"
}

{
  "$defs": {
    "RemapPeak": {
      "description": "One ReMap TF ChIP-seq binding peak record.",
      "properties": {
        "tf_name": {
          "description": "Gene symbol of the transcription factor (e.g. 'FOXA1').",
          "title": "Tf Name",
          "type": "string"
        },
        "chrom": {
          "description": "Chromosome (e.g. 'chr8').",
          "title": "Chrom",
          "type": "string"
        },
        "start": {
          "description": "0-based genomic start coordinate.",
          "title": "Start",
          "type": "integer"
        },
        "end": {
          "description": "Genomic end coordinate (exclusive).",
          "title": "End",
          "type": "integer"
        },
        "experiment": {
          "description": "Experiment identifier (e.g. ENCSR accession) or 'unknown'.",
          "title": "Experiment",
          "type": "string"
        },
        "cell_type": {
          "default": "unknown",
          "description": "Cell type or tissue of the ChIP-seq experiment.",
          "title": "Cell Type",
          "type": "string"
        },
        "score": {
          "default": 0,
          "description": "Peak score (higher = more significant). 0.0 when not reported.",
          "title": "Score",
          "type": "number"
        }
      },
      "required": [
        "tf_name",
        "chrom",
        "start",
        "end",
        "experiment"
      ],
      "title": "RemapPeak",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.remap_tfbs``.",
  "properties": {
    "query": {
      "description": "The query that was made: either the TF symbol or the genomic region.",
      "title": "Query",
      "type": "string"
    },
    "query_mode": {
      "description": "Query mode used: 'tf_symbol' or 'region'.",
      "title": "Query Mode",
      "type": "string"
    },
    "peaks": {
      "description": "ReMap TF binding peaks matching the query, capped at ``limit``. Sorted by score descending (highest score first).",
      "items": {
        "$ref": "#/$defs/RemapPeak"
      },
      "title": "Peaks",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no peaks were found for the given query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "ReMap (remap.univ-amu.fr)",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "query",
    "query_mode"
  ],
  "title": "ForgeRemapTfbsOut",
  "type": "object"
}