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