jaspar_tfbs read

{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.jaspar_tfbs``.",
  "properties": {
    "tf_names": {
      "description": "Transcription factor names to query (e.g. ``['TP53', 'CTCF']``). Between 1 and 10 names per call.",
      "items": {
        "type": "string"
      },
      "title": "Tf Names",
      "type": "array"
    },
    "species": {
      "default": 9606,
      "description": "NCBI taxon ID for the species to query. Default 9606 (Homo sapiens). Use 10090 for Mus musculus.",
      "minimum": 1,
      "title": "Species",
      "type": "integer"
    },
    "collection": {
      "default": "CORE",
      "description": "JASPAR collection to search. Default ``'CORE'`` (manually reviewed, non-redundant profiles). Other collections: ``'UNVALIDATED'``, ``'PHYLOFACTS'``, ``'CNE'``, ``'POLII'``, ``'FAM'``, ``'PBM'``, ``'PBM_HOMEO'``, ``'PBM_HLH'``.",
      "maxLength": 32,
      "title": "Collection",
      "type": "string"
    },
    "min_ic": {
      "default": 8,
      "description": "Minimum total information content (bits) to include a profile. Profiles with ``information_content < min_ic`` are excluded. Default 8.0 bits (filters low-specificity matrices).",
      "minimum": 0,
      "title": "Min Ic",
      "type": "number"
    }
  },
  "required": [
    "tf_names"
  ],
  "title": "ForgeJASPARTFBSIn",
  "type": "object"
}

{
  "$defs": {
    "JASPARProfile": {
      "description": "One JASPAR 2024 transcription factor binding site profile.",
      "properties": {
        "matrix_id": {
          "description": "JASPAR matrix accession (e.g. 'MA0106.3').",
          "title": "Matrix Id",
          "type": "string"
        },
        "tf_name": {
          "description": "Official transcription factor name.",
          "title": "Tf Name",
          "type": "string"
        },
        "tf_class": {
          "description": "TF structural class (e.g. 'Zinc-coordinating').",
          "title": "Tf Class",
          "type": "string"
        },
        "tf_family": {
          "description": "TF family (e.g. 'p53').",
          "title": "Tf Family",
          "type": "string"
        },
        "information_content": {
          "description": "Total information content of the position weight matrix (bits).",
          "title": "Information Content",
          "type": "number"
        },
        "n_sequences": {
          "description": "Number of binding sequences used to build this profile.",
          "title": "N Sequences",
          "type": "integer"
        },
        "jaspar_url": {
          "description": "Direct URL to the JASPAR matrix page.",
          "title": "Jaspar Url",
          "type": "string"
        }
      },
      "required": [
        "matrix_id",
        "tf_name",
        "tf_class",
        "tf_family",
        "information_content",
        "n_sequences",
        "jaspar_url"
      ],
      "title": "JASPARProfile",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.jaspar_tfbs``.",
  "properties": {
    "profiles": {
      "description": "JASPAR profiles matching the query, filtered by ``min_ic``. Multiple profiles per TF are possible when more than one matrix version or cell-type-specific variant exists.",
      "items": {
        "$ref": "#/$defs/JASPARProfile"
      },
      "title": "Profiles",
      "type": "array"
    },
    "not_found": {
      "description": "TF names for which no profiles were found, or all profiles fell below the ``min_ic`` threshold.",
      "items": {
        "type": "string"
      },
      "title": "Not Found",
      "type": "array"
    },
    "took_ms": {
      "description": "Wall-clock time for all upstream API calls (ms).",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeJASPARTFBSOut",
  "type": "object"
}