EnzymeML – a data exchange format for biocatalysis and enzymology

16 September 2021, Version 1
This content is an early or alternative research output and has not been peer-reviewed by Cambridge University Press at the time of posting.


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.


STRENDA Guidelines
research data management
FAIR data principles

Supplementary materials

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


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