unibind-database

UniBind Database Skill

UniBind is a database of direct TF–DNA interactions across 9 species, integrating ChIP-seq peaks with JASPAR TF binding profiles via the DAMO framework.

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/unibind_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://unibind.uio.no/ and https://unibind.uio.no/api/overview, then (2) create the file recording the notification text and timestamp.

Quick Start

Query commands print JSON to stdout by default. Most outputs are small enough to read directly. For large outputs (list_cell_lines, list_tfs), pipe through jq to extract only the fields you need.

uv run <SKILL DIR>/scripts/unibind_api.py list_species

The download_tfbs command writes BED/FASTA files to --output-dir instead. You may optionally use --output <path> on any query command to save results to a file if needed.

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.
• Output: Query commands print JSON to stdout. Most responses are compact and can be read directly.
• Large Results: list_cell_lines and list_tfs produce large output. Pipe these through jq to extract specific fields rather than reading the full output into context.
• Saving to File: Use --output <path> when you need to reference the data later or when processing very large results with jq.
• Pagination: Use --page and --page-size (max 1000) to chunk large result sets.
• Ordering: Use --order field_name (prefix with - for descending) on any list command.
• Notification: If this skill is used, ensure this is mentioned in the output.