Can I search for genes across different species?

Yes, scripts allow you to specify organisms by name (e.g., 'human') or Taxon ID to ensure precise results when searching by gene symbol.

Do I need an NCBI account to use this skill?

An account is not required for basic use, but registering for a free API key at NCBI is recommended to increase rate limits for batch processing.

How does this skill handle NCBI API rate limits?

The skill includes built-in rate limiting logic, supporting 3-5 requests per second by default and up to 10 requests per second if you provide a free NCBI API key.

What data formats are supported for gene retrieval?

You can retrieve data in JSON for programmatic use, XML for legacy systems, or FASTA and GenBank for sequence analysis workflows.

What is the difference between E-utilities and the Datasets API?

E-utilities is better for complex, cross-database searches, while the Datasets API is a newer, optimized interface specifically for retrieving gene metadata and sequences.

NCBI Gene Database Tools

Name: NCBI Gene Database Tools
Author: lifangda

bylifangda

•

Data Science & ML

Queries and retrieves genomic data from NCBI Gene databases using E-utilities and the modern Datasets API.

This skill empowers Claude to interact directly with NCBI's comprehensive genomic resources, providing specialized tools for searching gene nomenclature, chromosomal maps, biological pathways, and phenotypes. It streamlines complex bioinformatics workflows by wrapping NCBI’s E-utilities and Datasets APIs into optimized scripts for gene searching, detailed metadata retrieval, and high-throughput batch lookups. Whether you are performing functional analysis, validating gene lists, or extracting RefSeqs, this skill provides the necessary patterns for reliable and rate-limited genomic data access.

Key Features

01Advanced gene searching via E-utilities with complex filtering for symbols, organisms, and diseases.

02Streamlined metadata and sequence retrieval using the modern NCBI Datasets API.

03Efficient batch lookup processing with automated rate limiting and API key support.

04Multi-format output support including JSON, XML, GenBank, and FASTA for diverse analysis pipelines.

05Integrated access to Gene Ontology (GO) annotations, phenotypic data, and chromosomal mapping.

0616 GitHub stars

Use Cases

01Automating gene annotation and metadata extraction for bioinformatics research pipelines.

02Validating and cross-referencing large lists of gene identifiers across multiple organisms.

03Identifying gene sets associated with specific biological contexts, pathways, or disease phenotypes.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add lifangda/claude-plugins gene-database

For use in Claude.ai and ChatGPT

Download Skill