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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  
SUMMARY SABIO-RK is a curated database containing biochemical reactions and theirs kinetics.  ...  For the quantitative analysis of biochemical reactions by modelling their enzyme kinetics, reliable kinetic data for the individual reaction steps are essential.  ... 
doi:10.1093/nar/gkr1046 pmid:22102587 pmcid:PMC3245076 fatcat:rybadguwrbhaxne67gcy5w5h2y

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: Curated Kinetic Data of Biochemical Reactions

Ulrike Wittig
2009 Nature Precedings  
Summary 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  ...  databases in SABIO-RK user interface and SBML export Controlled Vocabularies in SABIO-RK Chemical compounds names Role of reaction participants (substrate, product, modifier) Defined reactions  ...  Analysis of Compound Names Access to SABIO-RK  ... 
doi:10.1038/npre.2009.3085.1 fatcat:t5wq2vocbjel5br6aetaoazpha

SABIO-RK: Access to Biochemical Reaction Kinetics Data

Martin Golebiewski, Martin Golebiewski
2011 Nature Precedings  
to SABIO-RK (currently implemented by platforms like JWS online or Virtual Cell) • Access restriction for sensitive data • Extended information in exported SBML SABIO-RK SBML Export SABIO-RK SBML  ...  entries can be exported in one SBML file  Data is annotated (RDF and SBOterms) according to MIRIAM  Annotations include SABIO-RK Ids (reaction and kineticlaw) for tracking  Optional normalization of  ... 
doi:10.1038/npre.2011.6506.1 fatcat:sgskzkratjazrlixq2eajozjme

SABIO-RK: Access to Biochemical Reaction Kinetics Data

Martin Golebiewski, Martin Golebiewski
2011 Nature Precedings  
to SABIO-RK (currently implemented by platforms like JWS online or Virtual Cell) • Access restriction for sensitive data • Extended information in exported SBML SABIO-RK SBML Export SABIO-RK SBML  ...  entries can be exported in one SBML file  Data is annotated (RDF and SBOterms) according to MIRIAM  Annotations include SABIO-RK Ids (reaction and kineticlaw) for tracking  Optional normalization of  ... 
doi:10.1038/npre.2011.6506 fatcat:f557lksjjjehrk3jt2aja2k6d4

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  
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  ...  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.  ...  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

Integration of SABIO-RK in workbenches for kinetic model design

Martin Golebiewski, Saqib Mir, Renate Kania, Olga Krebs, Andreas Weidemann, Ulrike Wittig, Isabel Rojas
2007 BMC Systems Biology  
To provide quantitative experimental data, we have developed SABIO-RK [1], a database system offering information about biochemical reactions and their corresponding kinetics.  ...  using or requiring kinetic data for biochemical reactions.  ...  To provide quantitative experimental data, we have developed SABIO-RK [1], a database system offering information about biochemical reactions and their corresponding kinetics.  ... 
doi:10.1186/1752-0509-1-s1-p4 fatcat:cfr4f2h3vfapled6fubhmlrsd4

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.  ...  Kinetic data of biochemical reactions are essential for the creation of kinetic models of biochemical networks.  ...  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: 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  
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  ...  SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.  ...  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

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.  ...  (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  ...  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

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

Matthias König
2016 F1000Research  
Wittig U, Kania R, Golebiewski M, et al.: SABIO-RK--database for biochemical reaction kinetics. Nucleic Acids Res. 2012; 40(Database issue): D790-D796.  ...  One of the main resources of such information is SABIO-RK, a curated database for kinetic data of biochemical reactions and their related information.  ...  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

Exchanging Experimental Kinetic Data via SabioML

Martin Golebiewski, Martin Golebiewski
2010 Nature Precedings  
Acknowledgements SABIO-RK Team  ...   Kinetic data from literature and directly from experiments merged with data describing biochemical reactions and pathways from other resources  Data about metabolic and signalling reactions, as well  ...  Compound • recommended name • synonymic names • IDs in external databases (KEGG, ChEBI, PubChem ...) • additional information Developped for data import into the SABIO-RK database • Data schema mapped  ... 
doi:10.1038/npre.2010.5030 fatcat:2cgcw3nurbh6zdtpy7nrdvd2ia

Exchanging Experimental Kinetic Data via SabioML

Martin Golebiewski, Martin Golebiewski
2010 Nature Precedings  
Acknowledgements SABIO-RK Team  ...   Kinetic data from literature and directly from experiments merged with data describing biochemical reactions and pathways from other resources  Data about metabolic and signalling reactions, as well  ...  Compound • recommended name • synonymic names • IDs in external databases (KEGG, ChEBI, PubChem ...) • additional information Developped for data import into the SABIO-RK database • Data schema mapped  ... 
doi:10.1038/npre.2010.5030.1 fatcat:qoy3npvkxvc7nfhyjy7w2wvyxu

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.  ...  However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters.  ...  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  
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  ...  NS also thanks Joseph Dada for assistance with the SBRML export.  ...  There exist several publicly available databases containing enzyme kinetics data that adhere to these recommendations, with BRENDA [6] , a database for enzyme functional data, and the biochemical reaction  ... 
doi:10.1111/j.1742-4658.2010.07778.x pmid:20738395 fatcat:k6plhlhxbffu5ncb5czuofdkhq
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