md_harmonize: A Python Package for Atom-Level Harmonization of Public Metabolic Databases

Huan Jin; Hunter N.B. Moseley

doi:10.3390/metabo13121199

md_harmonize: A Python Package for Atom-Level Harmonization of Public Metabolic Databases

Huan Jin
, Hunter N.B. Moseley

Producción científica: Article › revisión exhaustiva

6 Citas (Scopus)

Resumen

A major 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. The md_harmonize 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 md_harmonize 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.

Idioma original	English
Número de artículo	1199
Publicación	Metabolites
Volumen	13
N.º	12
DOI	https://doi.org/10.3390/metabo13121199
Estado	Published - dic 2023

Nota bibliográfica

Publisher Copyright:
© 2023 by the authors.

Financiación

The research was funded by the United States National Science Foundation (NSF), grant number 2020026.

Financiadores	Número del financiador
U.S. Department of Energy Chinese Academy of Sciences Guangzhou Municipal Science and Technology Project Oak Ridge National Laboratory Extreme Science and Engineering Discovery Environment National Science Foundation National Energy Research Scientific Computing Center National Natural Science Foundation of China	2020026
U.S. Department of Energy Chinese Academy of Sciences Guangzhou Municipal Science and Technology Project Oak Ridge National Laboratory Extreme Science and Engineering Discovery Environment National Science Foundation National Energy Research Scientific Computing Center National Natural Science Foundation of China

ODS de las Naciones Unidas

Este resultado contribuye a los siguientes Objetivos de Desarrollo Sostenible

Good health and well being

ASJC Scopus subject areas

Endocrinology, Diabetes and Metabolism
Biochemistry
Molecular Biology

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abstract = "A major 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. The md\_harmonize package utilizes a neighborhood-specific graph coloring method for generating a unique identifier for each compound via atom identifiers based on a compound{\textquoteright}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 md\_harmonize 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.",

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md_harmonize: A Python Package for Atom-Level Harmonization of Public Metabolic Databases

Resumen

Nota bibliográfica

Financiación

ODS de las Naciones Unidas

ASJC Scopus subject areas

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