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ENCODE (Encyclopedia of DNA Elements)

| Endpoint | Description | |----------|-------------| | `/search/?type=Experiment&format=json` | Search experiments | | `/experiments/{accession}/?format=json` | Specific experiment | | `/files/{accession}/?format=json` | File metadata | | `/biosamples/{accession}/?format=json` | Biosample info | | `/annotations/?format=json` | Search annotations |

Claude Code Knowledge Pack7/10/2026

Overview

ENCODE (Encyclopedia of DNA Elements)

Base URL

https://www.encodeproject.org

Auth

No auth required. Append ?format=json or set Accept: application/json.

Every portal URL returns JSON when requested with the right header.

Key Endpoints

EndpointDescription
/search/?type=Experiment&format=jsonSearch experiments
/experiments/{accession}/?format=jsonSpecific experiment
/files/{accession}/?format=jsonFile metadata
/biosamples/{accession}/?format=jsonBiosample info
/annotations/?format=jsonSearch annotations

Search Parameters

  • type — Experiment, File, Biosample, Annotation, etc.
  • assay_title — ChIP-seq, RNA-seq, ATAC-seq, etc.
  • target.label — target protein (e.g. CTCF, H3K27ac)
  • biosample_ontology.term_name — cell type
  • limit — results per page
  • field — specific fields to return

Example Calls

# ChIP-seq experiments for CTCF
https://www.encodeproject.org/search/?type=Experiment&assay_title=ChIP-seq&target.label=CTCF&format=json&limit=5

# Specific experiment
https://www.encodeproject.org/experiments/ENCSR000AAA/?format=json

# Files for an experiment
https://www.encodeproject.org/search/?type=File&dataset=/experiments/ENCSR000AAA/&format=json

Response Format

JSON-LD. Search: @graph array + total + facets. Use frame=object or frame=embedded to control depth.

Rate Limits

No published limits. Use limit= and field= to reduce payload.