unibind-database

1# UniBind Database Skill
2 
3UniBind is a database of direct TF–DNA interactions across 9 species,
4integrating ChIP-seq peaks with JASPAR TF binding profiles via the DAMO
5framework.
6 
7## Prerequisites
8 
91.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
10    `uv` is installed and on PATH.
112.  **User Notification**: If .licenses/unibind_database_LICENSE.txt does not
12    already exist in the workspace root directory then (1) prominently notify
13    the user to check the terms at https://unibind.uio.no/ and
14    https://unibind.uio.no/api/overview, then (2) create the file recording the
15    notification text and timestamp.
16 
17## Quick Start
18 
19Query commands print JSON to stdout by default. Most outputs are small enough to
20read directly. For large outputs (`list_cell_lines`, `list_tfs`), pipe through
21`jq` to extract only the fields you need.
22 
23```bash
24uv run <SKILL DIR>/scripts/unibind_api.py list_species
25```
26 
27The `download_tfbs` command writes BED/FASTA files to `--output-dir` instead.
28You may optionally use `--output <path>` on any query command to save results to
29a file if needed.
30 
31## Core Rules
32 
33-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
34    database rather than accessing the database directly. The scripts
35    automatically enforce the required rate limit gracefully.
36-   **Output**: Query commands print JSON to stdout. Most responses are compact
37    and can be read directly.
38…