What data formats are supported for gene retrieval?

The skill supports multiple formats including JSON for programmatic use, XML for metadata, and FASTA or GenBank for sequence analysis.

Does this skill require an NCBI API key?

While optional, using an NCBI API key is recommended as it increases rate limits from 3 to 10 requests per second, which is essential for batch processing.

Can I search for genes in specific organisms?

Yes, you can filter searches by organism using common names like 'human' or scientific names like 'Mus musculus' to ensure precise results.

How does the skill handle batch gene lookups?

It includes a dedicated batch lookup script that processes multiple gene symbols or IDs simultaneously while automatically managing API rate limits.

NCBI Gene Database Explorer

Name: NCBI Gene Database Explorer
Author: K-Dense-AI

byK-Dense-AI

•

2,188

Data Science & ML

Integrates NCBI Gene data access into Claude for querying sequences, functional annotations, and genomic metadata.

About

This skill empowers Claude to interact directly with the NCBI Gene database, providing a robust interface for retrieving high-fidelity genomic information including nomenclature, reference sequences (RefSeqs), chromosomal maps, and functional pathways. By leveraging both the traditional E-utilities and the modern NCBI Datasets API, it enables researchers and bioinformaticians to perform complex biological queries, automate batch gene lookups, and extract structured metadata for scientific research, annotation pipelines, and data analysis directly within their coding environment.

Key Features

Retrieve detailed metadata including RefSeqs, GO terms, and phenotype associations
Cross-reference gene identifiers across diverse species and genomic resources
2,188 GitHub stars
Support for multiple formats including JSON, XML, GenBank, and FASTA
Search genes by symbol, name, chromosomal location, or biological context
Automate high-throughput batch gene lookups with built-in rate limiting

Use Cases

Automating gene annotation and metadata extraction for bioinformatics pipelines
Retrieving transcript and protein sequences for specific genetic variants or pathways
Validating and cross-referencing large gene lists for differential expression studies

About

Key Features

Retrieve detailed metadata including RefSeqs, GO terms, and phenotype associations
Cross-reference gene identifiers across diverse species and genomic resources
2,188 GitHub stars
Support for multiple formats including JSON, XML, GenBank, and FASTA
Search genes by symbol, name, chromosomal location, or biological context
Automate high-throughput batch gene lookups with built-in rate limiting

Use Cases

Automating gene annotation and metadata extraction for bioinformatics pipelines
Retrieving transcript and protein sequences for specific genetic variants or pathways
Validating and cross-referencing large gene lists for differential expression studies