gene-database

# NCBI Gene Database ## Overview NCBI Gene is the authoritative curated database for gene-centric information, covering 1M+ genes across hundreds of thousands of taxa. Each gene record includes the official symbol, aliases, full name, functional summary, genomic coordinates (GRCh38/GRCh37), RefSeq accessions, GO annotations, interaction partners, and links to related databases. Access is free via E-utilities REST API (no API key required, though recommended). ## When to Use - Resolving gene aliases and synonyms to the current official HGNC/NCBI symbol - Fetching the NCBI Gene ID (integer) for a gene symbol for downstream API calls (e.g., dbSNP, ClinVar, GEO) - Retrieving curated gene summaries and function descriptions programmatically - Pulling RefSeq mRNA (NM_) and protein (NP_) accessions associated with a gene - Querying GO functional annotations (Biological Process, Molecular Function, Cellular Component) - Finding orthologs across species via the NCBI Datasets v2 orthologs endpoint (legacy E-utilities `gene_gene_homolog` retired with HomoloGene in 2019) - For expression profiles across conditions use `geo-database`; for variant annotations use `clinvar-database` or `ensembl-database` ## Prerequisites - **Python packages**: `requests`, `xml.etree.ElementTree` (stdlib), `pandas` (optional) - **Data requirements**: gene symbols, NCBI Gene IDs, or tax IDs - **Environment**: internet connection; NCBI email required (set `email` parameter) - **Rate limits**: 3 req/s una...