Cortexa research tool·genomics·epigenomics

ENCODE Search Annotations

Search ENCODE annotations including candidate cis-Regulatory Elements (cCREs), chromatin states, and imputed signals. cCREs are classified as promoter-like (PLS), proximal enhancer-like (pELS), distal enhancer-like (dELS), DNase-H3K4me3 (DNase-H3K4me3), and CTCF-only. Chromatin state annotations use ChromHMM models to segment the genome into functional states. Use this to find regulatory element annotations for specific biosamples or genome assemblies.

Livelast probed 2026-05-01 01:00Z· 674msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 674ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "annotation_type": {
      "default": "candidate Cis-Regulatory Elements",
      "description": "Annotation type filter. Options: 'candidate Cis-Regulatory Elements' (cCREs), 'chromatin state' (ChromHMM), 'imputed signal' (predicted epigenetic marks). Default: cCREs.",
      "type": "string"
    },
    "assembly": {
      "default": "GRCh38",
      "description": "Genome assembly (e.g., 'GRCh38', 'hg19', 'mm10').",
      "type": "string"
    },
    "biosample_term_name": {
      "description": "Biosample filter (e.g., 'K562', 'HepG2'). Leave empty for all.",
      "type": [
        "string",
        "null"
      ]
    },
    "limit": {
      "default": 25,
      "description": "Maximum number of results.",
      "maximum": 100,
      "minimum": 1,
      "type": "integer"
    },
    "organism": {
      "default": "Homo sapiens",
      "description": "Organism scientific name.",
      "type": "string"
    }
  },
  "type": "object"
}

Examples (1)

Default ENCODE Search Annotations call

public-safeinput

{
  "limit": 3
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_ENCODE_search_annotations
Tool name: ENCODE_search_annotations
Added: 2026-05-01 00:58Z
Tags: tooluniverse

ENCODE Search Annotations

Livelast probed 2026-05-01 01:00Z· 674msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "annotation_type": { "default": "candidate Cis-Regulatory Elements", "description": "Annotation type filter. Options: 'candidate Cis-Regulatory Elements' (cCREs), 'chromatin state' (ChromHMM), 'imputed signal' (predicted epigenetic marks). Default: cCREs.", "type": "string" }, "assembly": { "default": "GRCh38", "description": "Genome assembly (e.g., 'GRCh38', 'hg19', 'mm10').", "type": "string" }, "biosample_term_name": { "description": "Biosample filter (e.g., 'K562', 'HepG2'). Leave empty for all.", "type": [ "string", "null" ] }, "limit": { "default": 25, "description": "Maximum number of results.", "maximum": 100, "minimum": 1, "type": "integer" }, "organism": { "default": "Homo sapiens", "description": "Organism scientific name.", "type": "string" } }, "type": "object" }