md_harmonize: a Python package for atom-level harmonization of public metabolic databases

Abstract

AbstractSummaryA big challenge to integrating public metabolic resources is the use of different nomenclatures by individual databases. This paper presents md_harmonize, an open-source Python package for harmonizing compounds and metabolic reactions across various metabolic databases. md_harmonize utilizes a neighborhood-specific graph coloring method for generating a unique identifier for each compound via atom identifiers based on the compound structure. The resulting harmonized compounds and reactions can be used to construct metabolic networks and models for various downstream analyses, including metabolic flux analysis.AvailabilityThe md_harmonize package is implemented in Python and freely available athttps://github.com/MoseleyBioinformaticsLab/md_harmonizeContacthunter.moseley@uky.eduSupplementary informationSupplementary data are available athttps://doi.org/10.6084/m9.figshare.21699683.