EnzymeML: FAIR data management in biocatalysis

Jürgen Pleiss

University of Stuttgart, Germany

Bio

Jürgen Pleiss obtained his PhD degree from the University of Tübingen under the supervision of Fritz Jähnig (Max-Planck-Institute of Biology).

He then joined the company Biostructure S.A., Strasbourg, to develop software for protein modelling.

Since 1995, he is head of the bioinformatics group at the Institute of Biochemistry and Technical Biochemistry (University of Stuttgart), where he obtained his Habilitation in 2001.

His research activities focus on enzyme design by combining bioinformatics and molecular simulation methods, and on the application of computational biology in white and red biotechnology.

Abstract

Enzyme catalysis provides a powerful toolbox for novel, sustainable synthesis routes and innovative solutions for bio-based chemistry. A comprehensive biochemical characterization of the desired enzyme-catalyzed reaction is essential and provides the basis for enzyme engineering and process development. Standardization of reporting of enzymatic data and metadata is considered as pivotal to accelerating bioprocess development and reducing costs. Meta-research studies suggest the lack of standardization to report and share experimental protocols, results, and data as one of the causes of the reproducibility crisis in the biomedical sciences.

As first steps for the standardized reporting of enzyme function data, the enzymology and biocatalysis community has established the Standards for Reporting Enzymology Data (STRENDA) Guidelines, the STRENDA DB as a public database to make enzymatic data findable and accessible, and the XML–based data exchange format EnzymeML to make enzymatic data interoperable and reusable. An Application Programming Interface facilitates the integration of applications such as electronic lab notebooks, modelling platforms, or databases. Thus, EnzymeML enables a reproducible and scalable documentation of biocatalytic data according to the F.A.I.R. principles.

EMMC2021-S07-Pleiss-Abstract

EMMC ASBL
European Materials Modelling Council
Silversquare Stéphanie
Avenue Louise 54
1050 Brussels
CBE no: 0731 621 312
contact@emmc.eu
chevron-down