{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:47:41Z","timestamp":1753876061392,"version":"3.41.2"},"reference-count":10,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T00:00:00Z","timestamp":1680307200000},"content-version":"vor","delay-in-days":90,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["031L0178"],"award-info":[{"award-number":["031L0178"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007316","name":"Klaus Tschira Stiftung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007316","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,31]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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.<\/jats:p><jats:p>Database URL https:\/\/sabiork.h-its.org\/<\/jats:p>","DOI":"10.1093\/database\/baad011","type":"journal-article","created":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T06:08:50Z","timestamp":1680329330000},"source":"Crossref","is-referenced-by-count":1,"title":["Improved insights into the SABIO-RK database via visualization"],"prefix":"10.1093","volume":"2023","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5034-730X","authenticated-orcid":false,"given":"Dorotea","family":"Duda\u0161","sequence":"first","affiliation":[{"name":"Scientific Databases and Visualization, Heidelberg Institute for Theoretical Studies (HITS gGmbH) , Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9077-5664","authenticated-orcid":false,"given":"Ulrike","family":"Wittig","sequence":"additional","affiliation":[{"name":"Scientific Databases and Visualization, Heidelberg Institute for Theoretical Studies (HITS gGmbH) , Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany"}]},{"given":"Maja","family":"Rey","sequence":"additional","affiliation":[{"name":"Scientific Databases and Visualization, Heidelberg Institute for Theoretical Studies (HITS gGmbH) , Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany"}]},{"given":"Andreas","family":"Weidemann","sequence":"additional","affiliation":[{"name":"Scientific Databases and Visualization, Heidelberg Institute for Theoretical Studies (HITS gGmbH) , Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany"}]},{"given":"Wolfgang","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Scientific Databases and Visualization, Heidelberg Institute for Theoretical Studies (HITS gGmbH) , Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany"}]}],"member":"286","published-online":{"date-parts":[[2023,3,31]]},"reference":[{"key":"2023040106083471400_","doi-asserted-by":"crossref","first-page":"D656","DOI":"10.1093\/nar\/gkx1065","article-title":"SABIO-RK: an updated resource for manually curated biochemical reaction kinetics","volume":"46","author":"Wittig","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023040106083471400_","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkaa1100","article-title":"UniProt: the universal protein knowledgebase in 2021","volume":"49","author":"The UniProt Consortium","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023040106083471400_","doi-asserted-by":"crossref","first-page":"D498","DOI":"10.1093\/nar\/gkaa1025","article-title":"BRENDA, the ELIXIR core data resource in 2021: new developments and updates","volume":"49","author":"Chang","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023040106083471400_","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.jbiotec.2017.04.020","article-title":"The BRENDA enzyme information system-from a database to an expert system","volume":"261","author":"Schomburg","year":"2017","journal-title":"J. Biotechnol."},{"article-title":"Information Visualization","year":"1999","author":"Card","key":"2023040106083471400_"},{"key":"2023040106083471400_","article-title":"Grand challenges in bioinformatics data visualization","volume":"1","author":"O\u2019Donoghue","year":"2021","journal-title":"Front. Bioinform."},{"article-title":"Navio - A Visualization Widget to Understand and Navigate Your Data","year":"2018","author":"G\u00f3mez","key":"2023040106083471400_"},{"key":"2023040106083471400_","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1021\/bi00530a023","article-title":"Stereospecificity of (E)- and (Z)-phosphoenol-alpha-ketobutyrate with chicken liver phosphoenolpyruvate carboxykinase and related phosphoenolpyruvate-utilizing enzymes","volume":"21","author":"Duffy","year":"1982","journal-title":"Biochemistry"},{"key":"2023040106083471400_","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.bpc.2015.06.010","article-title":"A new model for the aerobic metabolism of yeast allows the detailed analysis of the metabolic regulation during glucose pulse","volume":"206","author":"Kesten","year":"2015","journal-title":"Biophys. Chem."},{"key":"2023040106083471400_","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.bpc.2018.08.004","article-title":"An empirical analysis of enzyme function reporting for experimental reproducibility: missing\/incomplete information in published papers","volume":"242","author":"Halling","year":"2018","journal-title":"Biophys. Chem."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baad011\/49720385\/baad011.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baad011\/49720385\/baad011.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,8]],"date-time":"2023-12-08T10:49:09Z","timestamp":1702032549000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baad011\/7098623"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,1]]},"references-count":10,"URL":"https:\/\/doi.org\/10.1093\/database\/baad011","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2023,1,1]]},"article-number":"baad011"}}