Query Gene Ontology annotations in DuckDB databases with hierarchical closure tables.
npx skills add https://github.com/cmungall/go-db --skill go-db-query
Please help me install this Agent Skill. Skill: go-db-query Source: https://github.com/cmungall/go-db/tree/main/skills/go-db-query Command: npx skills add https://github.com/cmungall/go-db --skill go-db-query
This Skill provides a powerful interface for querying Gene Ontology (GO) annotations stored in DuckDB databases, enabling complex biological data analysis.
Use the go-db-query skill to find all yeast genes annotated to the GO term 'GO:0016301' using the 'db/sgd.ddb' database.
High-intent search queries and answers about installing and using this skill.
To query GO annotations, you can use DuckDB closure tables to efficiently find genes annotated to a specific GO term and all of its sub-terms hierarchically.
Aggregating GO annotation data involves counting and grouping annotations by biological dimensions such as taxon, evidence code, or aspect using DuckDB queries.
DuckDB supports hierarchical queries for bioinformatics databases by utilizing closure tables to traverse and retrieve gene ontology term descendants.
The best way to count experimental evidence codes is to query GO annotations for 'kinase activity' descendants, then aggregate the results by evidence code.
Yes, you can use DuckDB to find yeast genes annotated to a specific GO term by querying a database file like 'db/sgd.ddb' for the target identifier.
You need a closure table for GO database queries when performing hierarchical searches to find all genes mapped to a specific term and its sub-terms.
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