gget

Query genomic data across multiple databases via CLI and Python interfaces.

52|6|Updated Nov 24, 2025

Search Tags:#bioinformatics #UniProt #BLAST #Ensembl #gget #OpenTargets

Ready to run

npx skills add https://github.com/ovachiever/droid-tings --skill gget

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: gget
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/gget
Command: npx skills add https://github.com/ovachiever/droid-tings --skill gget

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides a CLI and Python package to query a wide range of genomic, proteomic, and functional databases from Ensembl to AlphaFold, UniProt, ARCHS4, OpenTargets, and more, enabling rapid data gathering and integration.

Core Features & Use Cases

Single interface for many databases: Access 20+ data sources through a consistent API.
End-to-end workflows: From gene search to sequence retrieval, expression, and disease associations.
Batch and programmatic access: Use via CLI or Python for automation and pipelines.

Quick Start

Query Ensembl for a gene, fetch its protein sequence, and retrieve expression data for tissues.

Frequently Asked Questions about gget

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I query multiple genomic databases with a single command?▼

gget provides unified CLI and Python interfaces to access 20+ databases—Ensembl, UniProt, NCBI, RCSB PDB, ARCHS4, Open Targets, and others—through consistent commands, eliminating the need to learn separate APIs for each source.

Can I retrieve gene sequences and expression data in one workflow?▼

Yes. gget integrates gene search, sequence retrieval, and expression profiling across Ensembl, UniProt, and ARCHS4 in a single pipeline, supporting end-to-end analysis from ID lookup to tissue-level expression output.

What output formats does gget support for bioinformatics analysis?▼

gget exports results as JSON and CSV, enabling direct integration into downstream analysis pipelines and compatible with standard bioinformatics workflows.

Can I use gget for disease and drug association queries?▼

Yes. gget queries Open Targets and other integrated databases to retrieve disease associations, drug targets, and functional relationships alongside genomic data in programmatic or CLI mode.

Does gget work with batch queries and automation?▼

gget supports both CLI and Python package interfaces with flexible parameter handling for species, IDs, and sequence translation, enabling batch processing and pipeline automation.

What bioinformatics tasks can gget handle beyond gene lookup?▼

gget performs sequence alignment, enrichment analysis, expression profiling across tissues, protein structure queries via RCSB PDB and AlphaFold, and cross-database metadata retrieval.