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Abstract (Expand)

SABIO-RK is a database for biochemical reactions and their kinetics. Data in SABIO-RK are inherently multidimensional and complex. The complex relationships between the data are often difficult to follow or even not represented when using standard tabular views. With an increasing number of data points the mismatch between tables and insights becomes more obvious, and getting an overview of the data becomes harder. Such complex data benefit from being presented using specially adapted visual tools. Visualization is a natural and user-friendly way to quickly get an overview of the data and to detect clusters and outliers. Here, we describe the implementation of a variety of visualization concepts into a common interface within the SABIO-RK biochemical reaction kinetics database. For that purpose, we use a heat map, parallel coordinates and scatter plots to allow the interactive visual exploration of general entry-based information of biochemical reactions and specific kinetic parameter values. Database URL

Authors: D. Dudas, U. Wittig, M. Rey, A. Weidemann, W. Muller

Date Published: 31st Mar 2023

Publication Type: Journal

Abstract (Expand)

SABIO-RK represents a repository for structured, curated, and annotated data on reactions and their kinetics. The data are manually extracted from the scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions, and the data are made available to the public via a web-based search interface as well as easy-to-use JSON web services for programmatic access. Data are highly interlinked to external databases, ontologies, and controlled vocabularies. This includes cross-references with eg Uniprot, ChEBI, KEGG, BRENDA, Biomodels, and MetaNetX. In the past year we have worked on improving findability of SABIO-RK data as well as interoperability: SABIO-RK was extended to read the additional annotations in the EnzymeML data exchange format to allow the direct import of enzymology data from EnzymeML documents. SABIO-RK is part of the EnzymeML workflow to support the data transfer between experimental platforms, modelling tools and databases (Range et al. FEBS J 2021). In the BMBF-funded project SABIO-VIS we focused on visualizing SABIORK data for the purpose of interactive search and search refinement.

Authors: Andreas Weidemann, Dorotea Dudas, Maja Rey, Ulrike Wittig, Wolfgang Müller

Date Published: 1st Aug 2022

Publication Type: InCollection

Abstract (Expand)

Research projects such as the international COVID-19 Disease Map initiative and the German COVID-19 study hub of NFDI are supported by de.NBI-SysBio tools and services in organizing and sharing research data ’FAIRly‘. This is done via the data management platform FAIRDOMHub/SEEK which is quickly adapted to the users' needs. COVID-19 related literature is manually curated and used for basic research about the curation process of SABIO-RK to provide the research community with high quality kinetics data.

Authors: Maja Rey, Andreas Weidemann, Ulrike Wittig, Dorotea Dudas, Sucheta Ghosh, Martin Golebiewski, Xiaoming Hu, Wolfgang Müller

Date Published: 2021

Publication Type: Booklet

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