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go-db-query

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Query GO annotations with DuckDB

Data & Analytics#go#bioinformatics#duckdb#database query#annotation#gene ontology
Authorcmungall
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This Skill provides a powerful interface for querying Gene Ontology (GO) annotations stored in DuckDB databases, enabling complex biological data analysis.

Core Features & Use Cases

  • Hierarchical Queries: Efficiently find genes annotated to GO terms and their descendants using closure tables.
  • Data Aggregation: Count and group annotations by various biological dimensions like taxon, evidence code, or aspect.
  • Use Case: Identify all human genes associated with 'kinase activity' and any of its sub-terms, then count how many of these annotations use experimental evidence codes.

Quick Start

Use the go-db-query skill to find all yeast genes annotated to the GO term 'GO:0016301' using the 'db/sgd.ddb' database.

Dependency Matrix

Required Modules

None required

Components

references

💻 Claude Code Installation

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Please help me install this Skill:
Name: go-db-query
Download link: https://github.com/cmungall/go-db/archive/main.zip#go-db-query

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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