Can I perform bulk queries for multiple genes at once?

Yes, the batch_gene_lookup script is designed specifically to process lists of gene symbols or IDs efficiently while handling API constraints.

How does this skill handle NCBI rate limits?

The skill includes logic to manage rate limits automatically, supporting 3-5 requests per second by default and up to 10 requests per second when a personal NCBI API key is provided.

Can I search for genes across different species?

Yes, you can specify organisms or taxa (e.g., 'human', 'Mus musculus') to filter results and ensure you are retrieving data for the correct species.

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

E-utilities is better for complex cross-database queries and traditional formats, while the Datasets API is optimized for straightforward gene metadata and sequence retrieval in modern formats like JSON.

NCBI Gene Database Explorer

Name: NCBI Gene Database Explorer
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Queries and retrieves comprehensive gene information from NCBI databases for genomic research and functional analysis.

This skill empowers researchers and developers to programmatically interact with the NCBI Gene database using both E-utilities and the modern Datasets API. It enables advanced searching by gene symbols, IDs, and biological contexts like GO terms or phenotypes, facilitates batch lookups for large gene panels, and provides structured data including RefSeqs, chromosomal mappings, and pathway information directly within the Claude environment. Whether validating gene lists or building bioinformatics pipelines, this skill streamlines the process of fetching high-quality genomic metadata.

Key Features

01Dual-API support for NCBI E-utilities and modern Datasets API

02Comprehensive metadata retrieval including RefSeqs and GO annotations

03Advanced search by symbol, organism, chromosome, or phenotype

04Multiple output formats including JSON, XML, and FASTA

05Efficient batch lookup processing with automated rate limiting

060 GitHub stars

Use Cases

01Validating and cross-referencing large lists of gene symbols

02Automated gene annotation and functional analysis for research

03Building gene-specific datasets for bioinformatics and ML models

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos gene-database

For use in Claude.ai and ChatGPT

Download Skill