drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/encode.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
ENCODE (Encyclopedia of DNA Elements)		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/encode.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

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.