# Unibind Database

Queries the UniBind database for experimentally validated transcription factor (TF)...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Data and ML
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill unibind-database -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill unibind-database -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill unibind-database -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill unibind-database -g -a gemini-cli -y`

## Description

Queries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FASTA) for local analysis, or listing available datasets by species, cell line, or TF name. Don't use to query specific intervals, locations, genes, motif models or expression data.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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.

```bash
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

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/unibind_database/SKILL.md