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SABIO-RK--database for biochemical reaction kinetics

U. Wittig, R. Kania, M. Golebiewski, M. Rey, L. Shi, L. Jong, E. Algaa, A. Weidemann, H. Sauer-Danzwith, S. Mir, O. Krebs, M. Bittkowski (+3 others)
2011 Nucleic Acids Research  
DATA INPUT AND CURATION There are two different ways to insert kinetic data into SABIO-RK.  ...  SUMMARY SABIO-RK is a curated database containing biochemical reactions and theirs kinetics.  ... 
doi:10.1093/nar/gkr1046 pmid:22102587 pmcid:PMC3245076 fatcat:rybadguwrbhaxne67gcy5w5h2y

cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK [article]

Matthias König
2016 bioRxiv   pre-print
One of the main resources of such information is SABIO-RK, a curated database for kinetic data of biochemical reactions and their related information.  ...  In this work, I present cy3sabiork, an app for querying and visualization of kinetic data from SABIO-RK in Cytoscape.  ...  SABIORK is a manually curated database for kinetic data storing comprehensive information about biochemical reactions and their kinetic properties, with data manually extracted from the literature and  ... 
doi:10.1101/062091 fatcat:jkvmvi66wfhh7cpxapz73xbdi4

SABIO-RK: Curated Kinetic Data of Biochemical Reactions

Ulrike Wittig
2009 Nature Precedings  
Future Perspectives • SABIO-RK as platform for experimental kinetic data -Scientists producing the data can directly enter it into SABIO-RK • Input interface as storage and exchange tool for authors of  ...  curated database for biochemical reactions and their kinetics platform for kinetic data storage and exchange free available for academic use use of standard data formats, controlled vocabularies and ontologies  ...  Analysis of Compound Names Access to SABIO-RK  ... 
doi:10.1038/npre.2009.3085.1 fatcat:t5wq2vocbjel5br6aetaoazpha

Data extraction for the reaction kinetics database SABIO-RK

Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller
2014 Perspectives in Science  
Here we describe the data extraction and curation efforts needed for SABIO-RK and give recommendations for publishing kinetic data in a complete and structured manner.  ...  SABIO-RK (http://sabio.h-its.org/) is a web-accessible, manually curated database that has been established as a resource for biochemical reactions and their kinetic properties with a focus on supporting  ...  Acknowledgements The SABIO-RK project is financed by the Klaus Tschira Foundation (http://www.klaus-tschira-stiftung.de/), the German Federal Ministry of Education and Research (http://www.bmbf.de/) through  ... 
doi:10.1016/j.pisc.2014.02.004 fatcat:fn2cw4lzivcztcux7whqb4vpbq

SABIO-RK: a database for biochemical reactions and their kinetics

Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Ulrike Wittig
2007 BMC Systems Biology  
The system SABIO-RK is a web-accessible curated database offering information about biochemical reactions and their kinetic properties.  ...  User interface Users can access the SABIO-RK database by a web-based interface that allows the search for biochemical reactions and their kinetics by specifying characteristics of the reactions of interest  ...  The system SABIO-RK is a web-accessible curated database offering information about biochemical reactions and their kinetic properties.  ... 
doi:10.1186/1752-0509-1-s1-s6 fatcat:xguez7ksjjg3fhkeapvbydcmay

SABIO-RK: A data warehouse for biochemical reactions and their kinetics

Olga Krebs, Martin Golebiewski, Renate Kania, Saqib Mir, Jasmin Saric, Andreas Weidemann, Ulrike Wittig, Isabel Rojas
2007 Journal of Integrative Bioinformatics  
biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks.  ...  In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics), a curated database with information about  ...  Acknowledgements SABIO-RK is funded by the Klaus Tschira Foundation and partially by the German Research Council (BMBF).  ... 
doi:10.1515/jib-2007-49 fatcat:esupiapcqjedlfvk2ame6nsrku

cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK

Matthias König
2016 F1000Research  
One of the main resources of such information is SABIO-RK, a curated database for kinetic data of biochemical reactions and their related information.  ...  In this work, I present cy3sabiork, an app for querying and visualization of kinetic data from SABIO-RK in Cytoscape.  ...  A special thanks to the curation team of SABIO-RK including additional kinetic data in the database based on provided publications. Supplementary material  ... 
doi:10.12688/f1000research.9211.1 fatcat:gt5l6qcb3rag7jdlyaasyeabd4

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

Ulrike Wittig, Maja Rey, Andreas Weidemann, Renate Kania, Wolfgang Müller
2017 Nucleic Acids Research  
SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics.  ...  (vi) The newly established SABIO-RK Curation Service allows to respond to specific data requirements.  ...  ACKNOWLEDGEMENTS Over the years many people worked on SABIO-RK software and database development or contributed to the database content.  ... 
doi:10.1093/nar/gkx1065 pmid:29092055 pmcid:PMC5753344 fatcat:c6gwi35b3bdy3huhuo3hlabcg4

Systematic integration of experimental data and models in systems biology

Peter Li, Joseph O Dada, Daniel Jameson, Irena Spasic, Neil Swainston, Kathleen Carroll, Warwick Dunn, Farid Khan, Naglis Malys, Hanan L Messiha, Evangelos Simeonidis, Dieter Weichart (+9 others)
2010 BMC Bioinformatics  
This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results.  ...  Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources.  ...  Acknowledgements PL and NS thank Wolfgang Mueller, Martin Golebiewski and Saqib Mir for providing technical support to SABIO-RK.  ... 
doi:10.1186/1471-2105-11-582 pmid:21114840 pmcid:PMC3008707 fatcat:i7nesnamujf4hdvm2hgimn5req

Enzyme kinetics informatics: from instrument to browser

Neil Swainston, Martin Golebiewski, Hanan L. Messiha, Naglis Malys, Renate Kania, Sylvestre Kengne, Olga Krebs, Saqib Mir, Heidrun Sauer-Danzwith, Kieran Smallbone, Andreas Weidemann, Ulrike Wittig (+5 others)
2010 The FEBS Journal  
Acknowledgements The authors thank the EPSRC and BBSRC for their funding of the Manchester Centre for Integrative Systems Biology (http://www.mcisb.org), BBSRC ⁄ EPSRC grant BB ⁄ C008219 ⁄ 1, and the Klaus  ...  Tschira Foundation (KTF) and the German Federal Ministry of Education and Research (BMBF) for funding the Scientific Databases and Visualization group at the Heidelberg Institute for Theoretical Studies  ...  Upon submission, the data are held in a gatekeeper database that can only be accessed by the submitter and curators of SABIO-RK.  ... 
doi:10.1111/j.1742-4658.2010.07778.x pmid:20738395 fatcat:k6plhlhxbffu5ncb5czuofdkhq

Normalization and Matching of Chemical Compound Names

Martin Golebiewski, Martin Golebiewski, Jasmin Šarić, Henriette Engelken, Meik Bittkowski, Ulrike Wittig, Wolfgang Müller, Isabel Rojas
2009 Nature Precedings  
KG, Biberach, Germany 1) Wittig U, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Anstein S, Saric J, Rojas I: "SABIO-RK: integration and curation of reaction kinetics data", Lecture Notes in Bioinformatics  ...  database system that we have developed to provide coherent experimental data, offers information about biochemical reactions and their corresponding kinetics [1,2].  ...  The normalization rules include, among others, reordering of substituent descriptions in the name and replacement of synonymous name constituents (e.g. equivalent trivial names).  ... 
doi:10.1038/npre.2009.3322 fatcat:l3x7qrtfmjdh7obreiqkau2idy

Social pathway annotation: extensions of the systems biology metabolic modelling assistant

I. Navas-Delgado, A. Real-Chicharro, M. A. Medina, F. Sanchez-Jimenez, J. F. Aldana-Montes
2010 Briefings in Bioinformatics  
The integration of data in the life sciences is a key component in the analysis of biological processes.  ...  These data may contain errors, but the curation of the vast amount of data generated in the 'omic' era cannot be done by individual researchers.  ...  Acknowledgements We would like to thank Daniel Pastor for his constant testing of the tool and advice, Amine Kerzazi for his continuous maintenance of the data wrappers and Ian Morilla for his invaluable  ... 
doi:10.1093/bib/bbq061 pmid:20965999 fatcat:3ls3d7nvj5edbaqrjaw3tc3pqa

Path2Models: large-scale generation of computational models from biochemical pathway maps

Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating (+14 others)
2013 BMC Systems Biology  
We produced models that combine data from KEGG PATHWAY, BioCarta, MetaCyc and SABIO-RK; According to the source data, three types of models are provided: kinetic, logical and constraint-based.  ...  However, mathematical models are still most often created de novo, based on reading the literature and processing pathway data manually.  ...  For instance, both their workflow and ours extract kinetic data from SABIO-RK. However, the aim of Li et al. was to provide full models, including parameterization and initial conditions.  ... 
doi:10.1186/1752-0509-7-116 pmid:24180668 pmcid:PMC4228421 fatcat:xihw5mql45gpzmiuc4svlr23nm

Mathematical modelling of proteome constraints within metabolism

Yu Chen, Jens Nielsen
2021 Current Opinion in Systems Biology  
Here we describe the concept of proteome constraints and review proteome-constrained GEMs, as well as their advantages and applications.  ...  ., low coverage of enzyme-specific turnover rates, and subsequently provide a few solutions to solve it. We end with a discussion on the trade-off between model complexity and capability.  ...  Acknowledgements This work was supported by the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 686070 and the Novo Nordisk Foundation (grant no.  ... 
doi:10.1016/j.coisb.2021.03.003 fatcat:zw56ooctu5a7vhvw354p37fwge

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

Andreas Dräger, Daniel C Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O Palsson, Andreas Zell
2015 BMC Systems Biology  
In addition, this program contains an integrated connection to the kinetics database SABIO-RK to obtain experimentally-derived rate laws when desired.  ...  Appropriate kinetic equations, based upon reaction rate laws, must be constructed and parameterized for each reaction.  ...  Acknowledgements The authors are grateful for contributions of (in alphabetical order) to Meike  ... 
doi:10.1186/s12918-015-0212-9 pmid:26452770 pmcid:PMC4600286 fatcat:ohvmzqevvndk7jz7wzjqzvyq4y
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