encode-ccres-database

1# ENCODE Database Skill
2 
3This skill allows you to query the ENCODE Registry of cCREs (candidate
4cis-Regulatory Elements) via the SCREEN GraphQL API. It helps identify
5functional non-coding DNA elements (like Promoters, Enhancers, and insulators)
6by analyzing biochemical signatures (DNase, H3K4me3, H3K27ac, CTCF).
7 
8## Prerequisites
9 
101.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
11    `uv` is installed and on PATH.
122.  **User Notification**: If .licenses/encode_ccres_database_LICENSE.txt does
13    not already exist in the workspace root directory then (1) prominently
14    notify the user to check the terms at
15    https://www.encodeproject.org/help/rest-api/, then (2) create the file
16    recording the notification text and timestamp.
17 
18## Core Rules
19 
20-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
21    database rather than accessing the database directly. The scripts
22    automatically enforce the required rate limit gracefully.
23-   **Parsing Output**: Do NOT use `cat` to read the entire JSON output file
24    into context, as it can be extremely large. You MUST use `jq` to efficiently
25    parse and extract relevant fields.
26-   **Notification**: If this skill is used, ensure this is mentioned in the
27    output.
28 
29### Quick Start
30 
31```bash
32# Search cCREs by coordinates
33uv run scripts/screen_api.py search --chromosome chr11 \
34  --start 5205263 --end 5207263 \
35  --output /tmp/search.json
36 
37# Get details for a specific cCRE
38…