Search and retrieve gene annotations from NCBI Gene via E-utilities and Datasets API.
npx skills add https://github.com/yf8578/clawomics --skill gene-database-yf8578
Please help me install this Agent Skill. Skill: gene-database Source: https://github.com/yf8578/clawomics/tree/main/skills/gene-database Command: npx skills add https://github.com/yf8578/clawomics --skill gene-database-yf8578
This Skill provides a programmatic interface to the NCBI Gene database, enabling users to efficiently search for genes, retrieve detailed information, and perform batch lookups, streamlining bioinformatics workflows.
Use the gene-database skill to search for the gene symbol 'BRCA1' in humans.
High-intent search queries and answers about installing and using this skill.
To query the NCBI gene database, you can search for genes by symbol, ID, or biological context using E-utilities like ESearch and ESummary. This retrieves detailed annotations including RefSeqs and GO terms.
The best way to retrieve detailed gene data for RNA-Seq analysis is performing batch lookups via the NCBI Datasets API to gather official symbols, descriptions, and known functions for differentially expressed genes.
Yes, you can perform batch lookups of multiple genes simultaneously using NCBI E-utilities and the Datasets API. This allows you to efficiently build annotation tables or validate gene lists.
Yes, querying the NCBI gene database supports searching by chromosomal location, disease association, or biological context. It uses ESearch and EFetch endpoints to filter and retrieve comprehensive gene data.
You can get RefSeqs and GO annotations for a specific gene ID by using the EFetch endpoint in the NCBI E-utilities API. This retrieves comprehensive gene data including chromosomal positions and detailed annotations.
Limitations of using the NCBI Datasets API for gene data retrieval include relying on external API rate limits and requiring programmatic access to handle E-utilities endpoints for comprehensive batch processing.
jimmc414Query NCBI Gene database via E-utilities and Datasets API for gene discovery.
silversteinSearch NCBI Gene records by symbol or ID and retrieve structured metadata.
ovachieverSearch GEO datasets and download gene expression data via E-utilities and GEOparse.
K-Dense-AIQuery NCBI Gene data via E-utilities and Datasets API for annotations.
