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

Data Science & ML

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

About

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.

Key Features

Support for multiple data formats including JSON, XML, GenBank, and FASTA
Seamless integration with NCBI E-utilities and the modern Datasets API
0 GitHub stars
Advanced search by gene symbol, organism, disease, or chromosome location
High-efficiency batch gene lookups with automated rate limit management
Comprehensive metadata retrieval including RefSeqs, GO annotations, and phenotypes

Use Cases

Investigating biological functions and pathway associations for specific gene candidates
Validating gene lists and cross-referencing identifiers across multiple species
Building automated gene annotation pipelines for large research datasets

About

Key Features

Support for multiple data formats including JSON, XML, GenBank, and FASTA
Seamless integration with NCBI E-utilities and the modern Datasets API
0 GitHub stars
Advanced search by gene symbol, organism, disease, or chromosome location
High-efficiency batch gene lookups with automated rate limit management
Comprehensive metadata retrieval including RefSeqs, GO annotations, and phenotypes

Use Cases

Investigating biological functions and pathway associations for specific gene candidates
Validating gene lists and cross-referencing identifiers across multiple species
Building automated gene annotation pipelines for large research datasets