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Review
. 2022 Oct;289(19):5864-5874.
doi: 10.1111/febs.16318. Epub 2021 Dec 26.

EnzymeML-a data exchange format for biocatalysis and enzymology

Jan Range  1 , Colin Halupczok  1 , Jens Lohmann  1 , Neil Swainston  2 , Carsten Kettner  3 , Frank T Bergmann  4 , Andreas Weidemann  5 , Ulrike Wittig  5 , Santiago Schnell  6   7 , Jürgen Pleiss  1
Affiliations
Free article
Review

EnzymeML-a data exchange format for biocatalysis and enzymology

Jan Range et al. FEBS J. 2022 Oct.
Free article

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.

Keywords: FAIR data principles; Python; Systems Biology Markup Language; XML; biocatalysis; bioinformatics; data exchange; enzymology; research data management.

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References

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