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gene-database

Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.

6,195stars743forksUpdated 1/16/2026

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About gene-database

The gene-database skill enables users to effectively query the NCBI Gene database using the E-utilities and Datasets API. This skill addresses the need for researchers and bioinformaticians to access detailed gene information, including gene sequences, nomenclature, and functional annotations. By leveraging this skill, users can efficiently retrieve relevant data for their genomic studies, facilitating a deeper understanding of gene functions and associations with various biological contexts.

Key features of this skill include the ability to search genes by symbol or ID, perform batch lookups for multiple genes, and retrieve comprehensive gene information in various formats. The skill supports complex queries and provides access to critical data such as RefSeqs, Gene Ontology annotations, and chromosomal locations. It is designed for individuals working in genomics, bioinformatics, and related fields who require a reliable method for gene data retrieval and analysis.

Use cases for the gene-database skill range from academic research to clinical applications, where understanding gene annotations and their functions is pivotal. Target users include researchers conducting functional analyses, geneticists validating gene panels, and educators teaching genomics. The skill streamlines the process of accessing extensive gene data, making it an invaluable resource for anyone involved in gene annotation and functional analysis.

FAQ

How do I start using the gene-database skill?

Begin by using the provided scripts for querying genes, such as 'query_gene.py' for searching genes by symbol or ID.

What APIs does the gene-database skill utilize?

The skill utilizes NCBI E-utilities and the Datasets API for accessing gene information.

Are there any rate limits when using the APIs?

Yes, without an API key, the rate limit is 3 requests/second for E-utilities and 5 requests/second for the Datasets API.

Can I use this skill for batch processing of gene data?

Yes, the skill includes a script for batch gene lookups to efficiently process multiple genes at once.

What output formats are supported by the API?

The APIs support output formats including JSON, XML, and plain text.

Install gene-database

Download and extract the skill files to your .claude/skills/ directory.

Quick Setup:

  1. Copy the skill folder to .claude/skills/
  2. Claude will automatically detect and use the skill