Catalysis

EnzymeML – a data exchange format for biocatalysis and enzymology

Authors

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, modelling tools, and databases. EnzymeML supports the scientific community by introducing a standardised data exchange format to make enzymatic data findable, accessible, interoperable, and reusable according to the FAIR data principles. An Application Programming Interface in Python and Java supports the integration of applications. 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 modelling using the modelling platform COPASI, and by uploading to the enzymatic reaction kinetics database SABIO-RK.

Content

Thumbnail image of Range_2021_EnzymeML.pdf

Supplementary material

Thumbnail image of Range_2021_EnzymeML_SI.pdf
SI to "EnzymeML - a data exchange format for biocatalysis and enzymology"
Supporting information to "EnzymeML - a data exchange format for biocatalysis and enzymology" 1. Structure of EnzymeML documents 2. API and thin API layer 3. Applications

Supplementary weblinks

EnzymeML
EnzymeML website: EnzymeML is a free and open XML-based format for a standardized monitoring and exchange of data on enzyme-catalyzed reactions according to the FAIR principles. The website hosts documents on EnzymeML, tools for research data management using EnzymeML, and more information about the EnzymeML project.