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quickgo-database

Map gene products to Gene Ontology terms via QuickGO and ECO REST APIs.

2.7k|283|Updated May 13, 2026
Search Tags:#gene ontology#functional annotation#quickgo#evidence & conclusion ontology#go slim#gene product mapping
One-click install
npx skills add https://github.com/google-deepmind/science-skills --skill quickgo-database-google-deepmind
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: quickgo-database
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/quickgo_database
Command: npx skills add https://github.com/google-deepmind/science-skills --skill quickgo-database-google-deepmind

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill helps you find and organize Gene Ontology (GO) and Evidence & Conclusion Ontology (ECO) information for genes and their products so you can understand gene functions from reliable ontology mappings.

Core Features & Use Cases

  • GO term exploration: Search GO terms and retrieve term definitions, synonyms, hierarchy relationships (ancestors/descendants/children), and GO slims for high-level summaries.
  • Functional annotation mapping: Search QuickGO annotations to connect gene products to biological processes, molecular functions, or cellular components, with optional evidence filtering to prefer experimental support.
  • Gene product resolution: Resolve common gene symbols to formal identifiers (e.g., UniProtKB IDs) before running annotation queries.

Quick Start

Use the quickgo-database skill to map the human UniProtKB gene product for PROC to experimental GO annotations by running the command: uv run scripts/quickgo_tool.py geneproduct search --query "PROC" --taxonId 9606 --limit 5 --output proc_id.json, then use the saved UniProtKB identifier to query annotations with uv run scripts/quickgo_tool.py annotation search --geneProductId "UniProtKB:P04070" --taxonId 9606 --evidenceCode "ECO:0000269" --limit 50 --output proc_annotations.json.

Frequently Asked Questions about quickgo-database

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

FAQPage Schema
How do I map a gene product to Gene Ontology functions using UniProtKB identifiers?▼

To map a gene product to Gene Ontology functions, you resolve the gene symbol to a formal UniProtKB identifier by querying the QuickGO API with a specific taxon ID, then use that identifier to retrieve associated GO term annotations.

How can I filter Gene Ontology annotations to only include experimental evidence?▼

You filter Gene Ontology annotations to experimental evidence by passing an Evidence & Conclusion Ontology (ECO) code, such as ECO:0000269, to exclude electronic annotations and retrieve only experimental records.

How do I retrieve ancestor and descendant relationships for a Gene Ontology term?▼

Retrieving ancestor and descendant relationships for a Gene Ontology term involves using ontology navigation features to query the hierarchy, returning the term definitions, synonyms, and parent-child structural connections.

Can I restrict QuickGO annotation queries to a specific taxon like human?▼

Yes, you can restrict QuickGO annotation queries to a specific taxon like human by providing the taxonomy ID, such as 9606 for human, directly in your gene product or annotation search parameters.

What are the limits for fetching Gene Ontology annotations from the QuickGO REST API?▼

The limits for fetching Gene Ontology annotations from the QuickGO REST API include a maximum of 100 results per page, requiring pagination handling and incremental JSON output storage via an output flag to respect rate limits.

What is a GO slim and when do I need it for functional annotation?▼

A GO slim provides a high-level summary of Gene Ontology functions by mapping specific detailed terms to broader categories, useful when you need to perform functional annotation workflows at a less granular biological level.

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