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

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