EnzymeML-a data exchange format for biocatalysis and enzymology.
FAIR data principles
Python
Systems Biology Markup Language
XML
biocatalysis
bioinformatics
data exchange
enzymology
research data management
Journal
The FEBS journal
ISSN: 1742-4658
Titre abrégé: FEBS J
Pays: England
ID NLM: 101229646
Informations de publication
Date de publication:
10 2022
10 2022
Historique:
revised:
15
11
2021
received:
22
09
2021
accepted:
09
12
2021
pubmed:
11
12
2021
medline:
6
10
2022
entrez:
10
12
2021
Statut:
ppublish
Résumé
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.
Types de publication
Journal Article
Review
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5864-5874Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/S004955/1
Pays : United Kingdom
Informations de copyright
© 2021 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.
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