encode-ccres-database

ENCODE Database Skill

This skill allows you to query the ENCODE Registry of cCREs (candidate cis-Regulatory Elements) via the SCREEN GraphQL API. It helps identify functional non-coding DNA elements (like Promoters, Enhancers, and insulators) by analyzing biochemical signatures (DNase, H3K4me3, H3K27ac, CTCF).

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
2. User Notification: If .licenses/encode_ccres_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.encodeproject.org/help/rest-api/, then (2) create the file recording the notification text and timestamp.

Core Rules

• Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
• Parsing Output: Do NOT use cat to read the entire JSON output file into context, as it can be extremely large. You MUST use jq to efficiently parse and extract relevant fields.
• Notification: If this skill is used, ensure this is mentioned in the output.

Quick Start

# Search cCREs by coordinates
uv run scripts/screen_api.py search --chromosome chr11 \
  --start 5205263 --end 5207263 \
  --output /tmp/search.json

# Get details for a specific cCRE
uv run scripts/screen_api.py details EH38E2941922 \
  --output /tmp/details.json

All subcommands write JSON to disk. Always save output in a temporary location like /tmp/.

Identifying High-Confidence ("Type A") Biosamples

Biosamples in ENCODE are often categorized by their data completeness. "Type A" (or high-confidence) biosamples are those that have experimental data for all four core epigenetic markers: DNase, H3K4me3, H3K27ac, and CTCF.

The biosamples and details commands automatically enrich their output with an is_type_a boolean flag for each biosample.