SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

Nucleic Acids Research
Ulrike WittigWolfgang Müller

Abstract

SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012). (i) The website has been completely revised and (ii) allows now also free text search for kinetics data. (iii) Additional interlinkages with other databases in our field have been established; this enables users to gain directly comprehensive knowledge about the properties of enzymes and kinetics beyond SABIO-RK. (iv) Vice versa, direct access to SABIO-RK data has been implemented in several systems biology tools and workflows. (v) On request of our experimental users, the data can be exported now additionally in spreadsheet formats. (vi) The newly established SABIO-RK Curation Service a...Continue Reading

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Citations

May 26, 2020·Database : the Journal of Biological Databases and Curation·Gemma L HollidayPatricia C Babbitt
Jul 11, 2020·Biotechnology and Bioengineering·Chao YeXiulai Chen
Jul 1, 2020·Journal of Integrative Bioinformatics·Dagmar WaltemathChris J Myers
Apr 25, 2018·Briefings in Bioinformatics·Marek OstaszewskiReinhard Schneider
Sep 4, 2020·PLoS Computational Biology·Susanne HollmannUNKNOWN Cost Action CA15110
Aug 28, 2020·Molecular Systems Biology·Sarah M KeatingUNKNOWN SBML Level 3 Community members
Dec 15, 2020·Journal of Biotechnology·Pranas GrigaitisNadine Veith
Mar 9, 2021·PLoS Computational Biology·Alexandre OliveiraOscar Dias
Jul 1, 2021·NPJ Systems Biology and Applications·Alina Renz, Andreas Dräger
Jan 26, 2022·MSystems·Philipp Wendering, Zoran Nikoloski

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