EnzymeML: seamless data flow and modeling of enzymatic data.

Reproducibility of Results Data Management Metadata Databases, Factual Kinetics

Journal

Nature methods

ISSN: 1548-7105

Titre abrégé: Nat Methods

Pays: United States

ID NLM: 101215604

Informations de publication

Date de publication:
03 2023

Historique:

received: 04 11 2020

accepted: 21 12 2022

pubmed: 10 2 2023

medline: 14 3 2023

entrez: 9 2 2023

Statut: ppublish

Résumé

The design of biocatalytic reaction systems is highly complex owing to the dependency of the estimated kinetic parameters on the enzyme, the reaction conditions, and the modeling method. Consequently, reproducibility of enzymatic experiments and reusability of enzymatic data are challenging. We developed the XML-based markup language EnzymeML to enable storage and exchange of enzymatic data such as reaction conditions, the time course of the substrate and the product, kinetic parameters and the kinetic model, thus making enzymatic data findable, accessible, interoperable and reusable (FAIR). The feasibility and usefulness of the EnzymeML toolbox is demonstrated in six scenarios, for which data and metadata of different enzymatic reactions are collected and analyzed. EnzymeML serves as a seamless communication channel between experimental platforms, electronic lab notebooks, tools for modeling of enzyme kinetics, publication platforms and enzymatic reaction databases. EnzymeML is open and transparent, and invites the community to contribute. All documents and codes are freely available at https://enzymeml.org .

Identifiants

DOI: 10.1038/s41592-022-01763-1 PMID: 36759590

pubmed: 36759590

doi: 10.1038/s41592-022-01763-1

pii: 10.1038/s41592-022-01763-1

doi:

Types de publication

Journal Article Research Support, U.S. Gov't, P.H.S. Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

Pagination

400-402

Subventions

Organisme : U.S. Department of Health & Human Services | U.S. Food and Drug Administration (U.S. Food & Drug Administration)

ID : Grant U01FD006484

Informations de copyright

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