Unibind Database
Google DeepMindOfficialPublished by Google DeepMind
- Skill
- Tool integration
- Science and research
- Apache-2.0
- Low risk
- Has scripts
AutoGineer summary
Written by AutoGineer from the skill’s own files, not by the author
The UniBind database skill provides a structured interface to access direct TF-DNA interaction datasets. It enables researchers to list available species, cell lines, and transcription factors, as well as filter datasets based on specific biological conditions or sources. The skill includes functionality to download binding site coordinates in BED or FASTA formats for local analysis, while enforcing rate limits and providing tools for handling large query results efficiently.
What it does
- Lists available species, cell lines, and transcription factors in the UniBind database.
- Filters and retrieves specific TF-DNA interaction datasets using various metadata parameters.
- Downloads binding site coordinates in BED or FASTA formats for downstream analysis.
- Provides dataset details including experimental source and collection information.
- Supports pagination and ordering for large result sets.
- Integrates with command-line tools to process and filter JSON output.
When to use it
- When you need to retrieve experimentally validated transcription factor binding site data.
- When you require BED or FASTA files for local genomic analysis.
- When you need to identify datasets associated with specific species, cell lines, or transcription factors.
- When you need to programmatically access UniBind metadata for research workflows.
Advantages
- Automated rate limiting ensures stable interaction with the UniBind API.
- Supports efficient handling of large datasets through command-line piping and pagination.
- Provides standardized access to validated TF-DNA interaction data.
- Facilitates reproducible research by enabling direct download of specific binding site files.
Usage examples
- “List all transcription factors available for Homo sapiens in the UniBind database.”
- The agent executes the list_tfs command and filters the output to display only the relevant transcription factor names.
- “Download the binding site data for CTCF in Homo sapiens from ENCODE as a BED file.”
- The agent identifies the correct dataset identifier and uses the download_tfbs command to save the BED file to the specified directory.
Install
Download the skill as a ZIP:
https://autogineer.com/agent-skills/google-deepmind/unibind-database/downloadUnzip it into the cross-client skills folder of your project:
mkdir -p .agents/skills && unzip unibind-database.zip -d .agents/skills
Documentation by Google DeepMind
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_speciesThe 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_linesandlist_tfsproduce large output. Pipe these throughjqto 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 withjq.Pagination: Use
--pageand--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.
Utility Scripts
Replace <SKILL DIR> with the absolute path to this skill's directory.
1. List Species
uv run <SKILL DIR>/scripts/unibind_api.py list_species2. List Collections
uv run <SKILL DIR>/scripts/unibind_api.py list_collections3. List Cell Lines & TFs (large output — use jp)
These commands return large datasets. Use uvx --from jmespath jp to extract
only the fields you need.
uv run <SKILL DIR>/scripts/unibind_api.py list_cell_lines | uvx --from jmespath jp "results[].name"
uv run <SKILL DIR>/scripts/unibind_api.py list_tfs | uvx --from jmespath jp "results[].tf_name"4. List and Filter Datasets (and Profile-Specific Datasets)
Filter datasets using the following arguments:
--species(e.g., "Homo sapiens")--tf-name(e.g., "CTCF")--cell-line(e.g., "mESC")--collection(e.g., Permissive, Robust)--search(a search term)--biological-condition(biological condition or source)--data-source(source of data, e.g., "ENCODE")--has-pvalue("true" or "false")--identifier(e.g., "GSE60130")--jaspar-id(JASPAR database profile matrix ID)--model(prediction model)--summary(summary filter)--threshold-pvalue(p-value threshold)
Use list_datasets for standard datasets, or list_specific_datasets for
profile-specific queries.
uv run <SKILL DIR>/scripts/unibind_api.py list_datasets --species "Homo sapiens" --tf-name "CTCF" --data-source "ENCODE"
uv run <SKILL DIR>/scripts/unibind_api.py list_specific_datasets --species "Mus musculus" --cell-line "mESC"5. Get Dataset Details
uv run <SKILL DIR>/scripts/unibind_api.py get_dataset "EXP047889.HMLE-Twist-ER_breast_cancer.SMAD3"6. Download TFBS Files (BED / FASTA)
Downloads all TFBS files for a dataset to a local directory. Use --format bed
(default) or --format fasta.
uv run <SKILL DIR>/scripts/unibind_api.py download_tfbs "EXP047889.HMLE-Twist-ER_breast_cancer.SMAD3" --output-dir /tmp/tfbs --format bedAnti-Patterns
DON'T attempt to use the UniBind API to query specific genomic intervals, locations, or genes.
DON'T guess or hallucinate genome coordinates. Always use
ensembl-databaseas an external check if you're pulling local BED tracks for offline bedtools intersection.DON'T use for motif models (PFMs). Use the jaspar-database skill instead.
DON'T use for gene expression data. UniBind only stores binding events.
DON'T assume tissue-specific expression from dataset lists alone.
DON'T use
catto read large JSON output files into context. The output is too large. Usejqor write your own code to parse the output files.
Files
- ATTRIBUTION.mdAdded by AutoGineer914 B
- LICENSELicence file added by AutoGineer11.1 KiB
- SKILL.md5.2 KiB
- references/citation.bib745 B
- scripts/unibind_api.pyScript12.8 KiB
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Requirements and compatibility
Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta
“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.
Needs: Needs Python
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Attribution and licence
- Published by
- Google DeepMind
- Publisher
- Google DeepMind (Official)
- Source
- google-deepmind/science-skills · skills/unibind_database · commit 4de6786
- Licence
- Apache License 2.0 (redistribution allowed)
- LICENSE (added by AutoGineer from LICENSE)
- ATTRIBUTION.md (written by AutoGineer)
- Synced
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