dbxrefs

dbxrefs is a Python package designed to facilitate the retrieval and analysis of cross-references in biological databases, particularly those related to gene and protein annotations. It serves as a bridge between various biological databases, allowing users to query and integrate data from sources such as UniProt, Ensembl, and Gene Ontology (GO) in a streamlined manner. The tool is particularly useful for researchers working with genomic or proteomic datasets, as it simplifies the process of mapping identifiers across different databases.

The package leverages the Biopython framework, which provides a robust foundation for handling biological data structures. dbxrefs automates the process of fetching cross-references by querying remote databases via their respective APIs or local files. It supports common identifier mappings, such as translating UniProt IDs to Ensembl gene IDs or retrieving GO terms associated with a protein. The tool also includes error handling mechanisms to manage cases where identifiers are missing or invalid, ensuring more reliable data processing.

dbxrefs is open-source and distributed under the MIT License, making it freely available for academic and commercial use. It is maintained by a community of bioinformatics developers and is regularly updated to incorporate new database mappings and improvements. The package is particularly valuable for pipelines that require consistent and up-to-date cross-references, as it reduces manual effort and minimizes errors in data integration. Users can install it via pip or conda, and documentation is provided to guide installation, usage, and customization for specific workflows.