Key points are not available for this paper at this time.
A major challenge to integrating public metabolic resources is the use of different nomenclatures by individual databases. This paper presents mdₕarmonize, an open-source Python package for harmonizing compounds and metabolic reactions across various metabolic databases. The mdₕarmonize package utilizes a neighborhood-specific graph coloring method for generating a unique identifier for each compound via atom identifiers based on a compound's chemical structure. The resulting harmonized compounds and reactions can be used for various downstream analyses, including the construction of atom-resolved metabolic networks and models for metabolic flux analysis. Parts of the mdₕarmonize package have been optimized using a variety of computational techniques to allow certain NP-complete problems handled by the software to be tractable for these specific use-cases. The software is available on GitHub and through the Python Package Index, with end-user documentation hosted on GitHub Pages.
Jin et al. (Sun,) studied this question.