Unibind Database
Queries the UniBind database for experimentally validated transcription factor (TF)...
Install
npx skills add google-deepmind/science-skills --skill unibind-database -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Data and ML
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Lightabout 1,217 tokens
- Runs scripts
- Yes, review before use
What it does
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.
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
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- 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.
