What data formats can I retrieve using the gene-database skill?

You can retrieve data in JSON, XML, GenBank, FASTA, and human-readable text formats depending on your research needs.

Is an NCBI API key required?

An API key is not required for basic use, but registering for a free key is recommended as it increases the rate limit from 3 to 10 requests per second.

Which NCBI APIs are supported by this skill?

The skill supports both NCBI E-utilities (ideal for complex cross-database queries) and the NCBI Datasets API (optimized for modern gene data and sequence retrieval).

Does this skill handle batch gene lookups?

Yes, it includes specialized scripts for batch processing multiple gene symbols or IDs simultaneously while managing API rate limits.

NCBI Gene Database Integration

Name: NCBI Gene Database Integration
Author: Activer007

byActiver007

0•

Data Science & ML

Queries the NCBI Gene database to retrieve comprehensive genetic information, sequences, and functional annotations via E-utilities and Datasets APIs.

The gene-database skill enables Claude to interact directly with the NCBI Gene database, providing a specialized interface for bioinformatics and genomic research. It leverages both the traditional E-utilities and the modern NCBI Datasets API to search for genes by symbol, ID, chromosomal location, or phenotype across diverse species. This skill is particularly useful for automating gene annotation tasks, retrieving reference sequences (RefSeqs), and performing functional analysis through Gene Ontology (GO) and pathway metadata retrieval. With built-in support for batch processing and rate-limit management, it streamlines the workflow for researchers and developers working with large-scale genomic data.

Key Features

01Comprehensive gene search by symbol, ID, phenotype, or biological context

02Efficient batch processing for high-volume gene identifier lookups

03Detailed metadata retrieval including RefSeqs, GO terms, and chromosomal maps

040 GitHub stars

05Dual API support for NCBI E-utilities and the modern Datasets API

06Automated rate limiting and error handling for reliable API communication

Use Cases

01Automating gene annotation and metadata collection for bioinformatics pipelines

02Batch validating gene lists and retrieving genomic coordinates for research

03Cross-referencing gene symbols with phenotypes and biological pathways

Key Features

01Comprehensive gene search by symbol, ID, phenotype, or biological context

02Efficient batch processing for high-volume gene identifier lookups

03Detailed metadata retrieval including RefSeqs, GO terms, and chromosomal maps

040 GitHub stars

05Dual API support for NCBI E-utilities and the modern Datasets API

06Automated rate limiting and error handling for reliable API communication

Use Cases

01Automating gene annotation and metadata collection for bioinformatics pipelines

02Batch validating gene lists and retrieving genomic coordinates for research

03Cross-referencing gene symbols with phenotypes and biological pathways