gene-database

What problem does it solve?

Manually searching and retrieving gene information from NCBI Gene, including sequences, annotations, and cross-references, is repetitive and inefficient. This Skill automates access to NCBI's E-utilities and Datasets API, simplifying gene annotation, functional analysis, and batch lookups, saving researchers valuable time.

Core Features & Use Cases

• Gene Search & Retrieval: Find genes by symbol or ID and fetch detailed information, including RefSeqs for transcripts/proteins, Gene Ontology (GO) annotations, and chromosomal locations.
• Batch Lookups: Efficiently process lists of genes with built-in rate limiting, ideal for annotating gene panels or large datasets.
• Functional & Pathway Analysis: Discover genes associated with specific biological contexts, pathways, or phenotypes by leveraging advanced query capabilities.
• Use Case: Provide a list of 50 gene symbols and automatically retrieve their NCBI Gene IDs, full descriptions, chromosomal locations, and associated RefSeq IDs, compiling a comprehensive annotation table for downstream analysis.

Quick Start

Search for BRCA1 in human using E-utilities

python scripts/query_gene.py --search "BRCA1" --organism "human"

Fetch comprehensive data for a gene ID (e.g., 672 for BRCA1) using Datasets API

python scripts/fetch_gene_data.py --gene-id 672

Perform a batch lookup for multiple genes from a file

(Assuming 'gene_list.txt' contains gene symbols like BRCA1, TP53, EGFR)

python scripts/batch_gene_lookup.py --file gene_list.txt --organism human --output results.json