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. 2018 Jan 4;46(D1):D656-D660.
doi: 10.1093/nar/gkx1065.

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

Ulrike Wittig  1 , Maja Rey  1 , Andreas Weidemann  1 , Renate Kania  2 , Wolfgang Müller  1
Affiliations

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

Ulrike Wittig et al. Nucleic Acids Res. .

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 allows to respond to specific data requirements.

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Figures

Figure 1.
Figure 1.
SABIO-RK statistics (status: September 2017).
Figure 2.
Figure 2.
Screenshots of SABIO-RK newly designed web-based search interface with query results for kinetics data in mammalian blood using ontology-based search (using NCBI taxonomy for organism and BTO for tissue).
Figure 3.
Figure 3.
Screenshot of SABIO-RK web-based search interface representing spreadsheet export functionality.
See this image and copyright information in PMC

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References

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    1. Wittig U., Kania R., Bittkowski M., Wetsch E., Shi L., Jong L., Golebiewski M., Rey M., Weidemann A., Rojas I. et al. . Data extraction for the reaction kinetics database SABIO-RK. Perspect. Sci. 2014; 1:33–40.
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