Does this skill require an NCBI API key?

An API key is not strictly required for low-volume queries, but it is highly recommended to increase rate limits from 3 to 10 requests per second for better performance.

Which organisms are supported?

The skill supports all organisms indexed in the NCBI Gene database, including humans, mice, zebrafish, and many other eukaryotes and prokaryotes.

What is the benefit of using the Datasets API over E-utilities?

The Datasets API is optimized for modern workflows, providing comprehensive gene metadata and sequences in a single, simplified request compared to the multi-step E-utilities process.

Can I search for genes by disease association?

Yes, you can use the E-utilities query patterns to search for genes associated with specific phenotypes or diseases, such as 'insulin[gene] AND diabetes[disease]'.

NCBI Gene Database Integration

Name: NCBI Gene Database Integration
Author: henriquescastilho

byhenriquescastilho

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Data Science & ML

Queries and retrieves comprehensive genetic information from the NCBI Gene database using E-utilities and Datasets APIs for biological research and annotation.

This skill empowers Claude to interact directly with the National Center for Biotechnology Information (NCBI) Gene database, enabling researchers and developers to search for genes by symbol or ID, fetch reference sequences (RefSeqs), and analyze functional annotations like Gene Ontology (GO) terms. It facilitates both complex E-utilities queries and streamlined data retrieval via the modern NCBI Datasets API, making it an essential tool for bioinformaticians performing gene characterization, batch validation, or pathway analysis. With built-in support for rate limiting and multiple output formats, it simplifies the process of integrating high-quality genomic data into scientific workflows.

Key Features

01Retrieve detailed metadata including RefSeqs, chromosomal maps, and GO annotations

02Dual API support for NCBI E-utilities and the modern Datasets API

031 GitHub stars

04Search genes by symbol, organism, biological context, or phenotype

05Perform high-throughput batch gene lookups with automated rate limiting

06Export data in multiple formats including JSON, XML, GenBank, and FASTA

Use Cases

01Automating gene annotation and functional analysis for genomic datasets

02Validating and cross-referencing large lists of gene symbols across organisms

03Retrieving reference sequences and mapping data for bioinformatic pipeline integration

Key Features

01Retrieve detailed metadata including RefSeqs, chromosomal maps, and GO annotations

02Dual API support for NCBI E-utilities and the modern Datasets API

031 GitHub stars

04Search genes by symbol, organism, biological context, or phenotype

05Perform high-throughput batch gene lookups with automated rate limiting

06Export data in multiple formats including JSON, XML, GenBank, and FASTA

Use Cases

01Automating gene annotation and functional analysis for genomic datasets

02Validating and cross-referencing large lists of gene symbols across organisms

03Retrieving reference sequences and mapping data for bioinformatic pipeline integration