Which API should I use: E-utilities or Datasets?

Use E-utilities for complex, cross-database searches and traditional formats. Use the Datasets API for modern, streamlined retrieval of gene metadata and sequences in a single request.

How do I increase the NCBI API request limit?

You can register for a free NCBI API key at their website. Including this key in your scripts increases your rate limit from 3 requests per second to 10 requests per second.

Can I perform batch lookups for multiple genes?

Yes, the skill includes a batch_gene_lookup.py script designed to process lists of gene symbols or IDs efficiently while handling rate limiting automatically.

What kind of biological data can I retrieve with this skill?

You can retrieve gene nomenclature, reference sequences (RefSeqs), chromosomal maps, biological pathways, genetic variations, phenotypes, and Gene Ontology (GO) annotations.

NCBI Gene Database Integration

Name: NCBI Gene Database Integration
Author: Sologa

bySologa

0•

데이터 과학 및 ML

Simplifies gene data retrieval and annotation by querying the NCBI Gene database via E-utilities and Datasets APIs.

The Gene Database skill enables Claude to interact seamlessly with NCBI's comprehensive genomic resources. It provides a robust interface for searching genes by symbol or ID, retrieving detailed metadata like RefSeqs and Gene Ontology (GO) annotations, and performing complex batch lookups. Whether you are conducting functional analysis, building gene annotation tables, or investigating biological pathways, this skill automates the data fetching process with built-in support for rate limiting and various output formats like JSON and XML, making it indispensable for bioinformatics workflows.

주요 기능

01Support for multiple data formats including JSON, XML, GenBank, and FASTA

02Seamless integration with NCBI E-utilities and the modern Datasets API

030 GitHub stars

04Advanced search by gene symbol, organism, disease, or chromosome location

05High-efficiency batch gene lookups with automated rate limit management

06Comprehensive metadata retrieval including RefSeqs, GO annotations, and phenotypes

사용 사례

01Investigating biological functions and pathway associations for specific gene candidates

02Validating gene lists and cross-referencing identifiers across multiple species

03Building automated gene annotation pipelines for large research datasets

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline gene-database

For use in Claude.ai and ChatGPT

Download Skill