Forge Tools unibind_tfbs

unibind_tfbs read

scidex.forge.unibind_tfbs

Query UniBind for high-confidence direct TF-DNA binding site datasets. UniBind (https://unibind.uio.no/) provides robust ChIP-seq-derived binding sites for hundreds of transcription factors across species. Input: tf_symbol (e.g. 'CTCF') and/or region (genome assembly 'hg38' or locus 'chr1:1000000-1100000'); at least one is required. Output: sites list with dataset_id, tf_name, cell_type, genome_assembly, n_peaks, experiment_id, and unibind_url. not_found=True when no datasets match. API: https://unibind.uio.no/api/v1/ — public, no auth required.

HTTP: POST /api/scidex/forge/unibind_tfbs

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.unibind_tfbs``.",
  "properties": {
    "tf_symbol": {
      "anyOf": [
        {
          "maxLength": 64,
          "minLength": 1,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Transcription factor gene symbol to query (e.g. ``'CTCF'``, ``'TP53'``). At least one of ``tf_symbol`` or ``region`` must be provided.",
      "title": "Tf Symbol"
    },
    "region": {
      "anyOf": [
        {
          "maxLength": 128,
          "minLength": 1,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Genomic region or genome assembly filter. Accepts either a compact locus (``'chr1:1000000-1100000'``) to restrict results to a genome assembly, or a bare assembly name (``'hg38'``, ``'mm10'``). At least one of ``tf_symbol`` or ``region`` must be provided.",
      "title": "Region"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of datasets to return. Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeUnibindTFBSIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "UnibindSite": {
      "description": "One UniBind robust TF-DNA binding site dataset record.",
      "properties": {
        "dataset_id": {
          "description": "UniBind internal dataset ID.",
          "title": "Dataset Id",
          "type": "integer"
        },
        "tf_name": {
          "description": "Transcription factor gene symbol (e.g. 'CTCF').",
          "title": "Tf Name",
          "type": "string"
        },
        "cell_type": {
          "default": "",
          "description": "Cell type or tissue of origin.",
          "title": "Cell Type",
          "type": "string"
        },
        "genome_assembly": {
          "default": "",
          "description": "Genome assembly (e.g. 'hg38', 'mm10').",
          "title": "Genome Assembly",
          "type": "string"
        },
        "n_peaks": {
          "default": 0,
          "description": "Number of robust binding peaks in this dataset.",
          "title": "N Peaks",
          "type": "integer"
        },
        "experiment_id": {
          "default": "",
          "description": "Source ChIP-seq experiment accession.",
          "title": "Experiment Id",
          "type": "string"
        },
        "unibind_url": {
          "default": "",
          "description": "Direct URL to the UniBind dataset page.",
          "title": "Unibind Url",
          "type": "string"
        }
      },
      "required": [
        "dataset_id",
        "tf_name"
      ],
      "title": "UnibindSite",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.unibind_tfbs``.",
  "properties": {
    "query": {
      "description": "Canonical query string (TF symbol and/or region).",
      "title": "Query",
      "type": "string"
    },
    "sites": {
      "description": "UniBind robust binding site dataset records matching the query.",
      "items": {
        "$ref": "#/$defs/UnibindSite"
      },
      "title": "Sites",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no matching datasets were found in UniBind.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "unibind",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call (ms).",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeUnibindTFBSOut",
  "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/unibind_tfbs' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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