Forge Tools encode_chipseq_experiments

encode_chipseq_experiments read

scidex.forge.encode_chipseq_experiments

Search ENCODE Project for ChIP-seq experiments targeting specific transcription factors or chromatin-binding proteins. Returns experiment accessions, TF target names, cell types, genome assemblies, and peak/signal file accessions. Distinct from encode_epigenomics (all assay types including histone marks, ATAC-seq) and encode_screen_ccres (regulatory elements). Focuses on TF binding site data for downstream motif and regulatory network analysis. API: https://www.encodeproject.org/ — public, no API key required.

HTTP: POST /api/scidex/forge/encode_chipseq_experiments

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_chipseq_experiments``.",
  "properties": {
    "gene_symbol": {
      "anyOf": [
        {
          "maxLength": 30,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Transcription factor or chromatin-binding protein gene symbol (e.g. ``CTCF``, ``TP53``, ``MYC``). Filters ChIP-seq experiments targeting this protein. At least one of ``gene_symbol`` or ``cell_type`` is required.",
      "title": "Gene Symbol"
    },
    "cell_type": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Cell line or tissue name (e.g. ``K562``, ``HepG2``, ``liver``). Matched against ENCODE's ``biosample_ontology.term_name``. At least one of ``gene_symbol`` or ``cell_type`` is required.",
      "title": "Cell Type"
    },
    "assembly": {
      "anyOf": [
        {
          "maxLength": 20,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Genome assembly filter (e.g. ``GRCh38``, ``hg19``, ``mm10``). When None, returns experiments from all assemblies.",
      "title": "Assembly"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of experiments to return (1–100). Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeENCODEChIPIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ENCODEChIPExperiment": {
      "description": "One ENCODE ChIP-seq experiment in the response.",
      "properties": {
        "accession": {
          "description": "ENCODE experiment accession (e.g. ``ENCSR000AEM``).",
          "title": "Accession",
          "type": "string"
        },
        "target": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "TF or protein target name (e.g. ``CTCF``, ``TP53``).",
          "title": "Target"
        },
        "biosample_term": {
          "default": "",
          "description": "Cell line or tissue name (e.g. ``K562``).",
          "title": "Biosample Term",
          "type": "string"
        },
        "biosample_type": {
          "default": "",
          "description": "Biosample classification (e.g. ``cell line``, ``tissue``).",
          "title": "Biosample Type",
          "type": "string"
        },
        "assembly": {
          "description": "Genome assemblies available for this experiment (e.g. ``['GRCh38', 'hg19']``).",
          "items": {
            "type": "string"
          },
          "title": "Assembly",
          "type": "array"
        },
        "status": {
          "default": "",
          "description": "Release status (e.g. ``released``, ``archived``).",
          "title": "Status",
          "type": "string"
        },
        "peak_files": {
          "description": "Peak call file accessions (ENCFF...) for this experiment.",
          "items": {
            "type": "string"
          },
          "title": "Peak Files",
          "type": "array"
        },
        "signal_files": {
          "description": "Signal/bigWig file accessions (ENCFF...) for this experiment.",
          "items": {
            "type": "string"
          },
          "title": "Signal Files",
          "type": "array"
        },
        "lab": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Submitting lab name.",
          "title": "Lab"
        },
        "encode_url": {
          "default": "",
          "description": "Direct ENCODE experiment page URL.",
          "title": "Encode Url",
          "type": "string"
        }
      },
      "required": [
        "accession"
      ],
      "title": "ENCODEChIPExperiment",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.encode_chipseq_experiments``.",
  "properties": {
    "experiments": {
      "description": "Matching ENCODE ChIP-seq experiments, capped at ``limit``.",
      "items": {
        "$ref": "#/$defs/ENCODEChIPExperiment"
      },
      "title": "Experiments",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total matching ENCODE ChIP-seq experiments.",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "title": "ForgeENCODEChIPOut",
  "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_chipseq_experiments' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.