EnzymeML-a data exchange format for biocatalysis and enzymology

Range, Jan, Halupczok, Colin, Lohmann, Jens, Swainston, Neil ORCID: 0000-0001-7020-1236, Kettner, Carsten, Bergmann, Frank T, Weidemann, Andreas, Wittig, Ulrike, Schnell, Santiago and Pleiss, Jurgen (2021) EnzymeML-a data exchange format for biocatalysis and enzymology. FEBS JOURNAL, 289 (19). pp. 5864-5874.

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Official URL: http://dx.doi.org/10.1111/febs.16318

Abstract

EnzymeML is an XML-based data exchange format that supports the comprehensive documentation of enzymatic data by describing reaction conditions, time courses of substrate and product concentrations, the kinetic model, and the estimated kinetic constants. EnzymeML is based on the Systems Biology Markup Language, which was extended by implementing the STRENDA Guidelines. An EnzymeML document serves as a container to transfer data between experimental platforms, modeling tools, and databases. EnzymeML supports the scientific community by introducing a standardized data exchange format to make enzymatic data findable, accessible, interoperable, and reusable according to the FAIR data principles. An application programming interface in Python supports the integration of software tools for data acquisition, data analysis, and publication. The feasibility of a seamless data flow using EnzymeML is demonstrated by creating an EnzymeML document from a structured spreadsheet or from a STRENDA DB database entry, by kinetic modeling using the modeling platform COPASI, and by uploading to the enzymatic reaction kinetics database SABIO-RK.

Item Type:	Article
Uncontrolled Keywords:	biocatalysis, bioinformatics, data exchange, enzymology, FAIR data principles, Python, research data management, Systems Biology Markup Language, XML
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User:	Symplectic Admin
Date Deposited:	18 May 2022 09:28
Last Modified:	18 Jan 2023 21:01
DOI:	10.1111/febs.16318
Open Access URL:	https://doi.org/10.1111/febs.16318
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3155033