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

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

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.