Book ChapterDOI
SABIO-RK: integration and curation of reaction kinetics data
Ulrike Wittig,Martin Golebiewski,Renate Kania,Olga Krebs,Saqib Mir,Andreas Weidemann,Stefanie Anstein,Jasmin Saric,Isabel Rojas +8 more
- pp 94-103
TLDR
SABIO-RK is a curated database with information about biochemical reactions and their kinetic properties, which contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions.Abstract:
Simulating networks of biochemical reactions require reliable kinetic data. In order to facilitate the access to such kinetic data we have developed SABIO-RK, a curated database with information about biochemical reactions and their kinetic properties. The data are manually extracted from literature and verified by curators, concerning standards, formats and controlled vocabularies. This process is supported by tools in a semi-automatic manner. SABIO-RK contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions. The type of the kinetic mechanism, modes of inhibition or activation, and corresponding rate equations are presented together with their parameters and measured values, specifying the experimental conditions under which these were determined. Links to other databases enable the user to gather further information and to refer to the original publication. Information about reactions and their kinetic data can be exported to an SBML file, allowing users to employ the information as the basis for their simulation models.read more
Citations
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Journal ArticleDOI
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
Janna Hastings,Paula de Matos,Adriano Dekker,Marcus Ennis,Bhavana Harsha,Namrata Kale,Venkatesh Muthukrishnan,Gareth Owen,Steve Turner,Mark Williams,Christoph Steinbeck +10 more
TL;DR: This work has completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology, and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them.
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CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks
TL;DR: In this article, the authors developed a modeling/simulating tool called CellDesigner, which can visualize, model, and simulate gene-regulatory and biochemical networks using SBML as a model-describing basis.
Journal ArticleDOI
Chemical Entities of Biological Interest: an update
Paula de Matos,Rafael Alcántara,Adriano Dekker,Marcus Ennis,Janna Hastings,Kenneth Haug,Inmaculada Spiteri,Steve Turner,Christoph Steinbeck +8 more
TL;DR: New features in ChEBI since the last NAR report in 2007 are reported, including substructure and similarity searching, a submission tool for authoring of ChE BI datasets by the community and a 30-fold increase in the number of chemical structures stored in Ch EBI.
Journal ArticleDOI
myExperiment: a repository and social network for the sharing of bioinformatics workflows
Carole Goble,Jiten Bhagat,Sergejs Aleksejevs,Don Cruickshank,Danius T. Michaelides,David Newman,Mark I. Borkum,Sean Bechhofer,Marco Roos,Peter Li,David De Roure +10 more
TL;DR: MyExperiment is an online research environment that supports the social sharing of bioinformatics workflows consisting of a series of computational tasks using web services, which may be performed on data from its retrieval, integration and analysis, to the visualization of the results.
Journal ArticleDOI
Controlled vocabularies and semantics in systems biology
Mélanie Courtot,Nick Juty,Christian Knüpfer,Dagmar Waltemath,Anna Zhukova,Andreas Dräger,Michel Dumontier,Andrew Finney,Martin Golebiewski,Janna Hastings,Stefan Hoops,Sarah M. Keating,Douglas B. Kell,Samuel Kerrien,James R. Lawson,Allyson L. Lister,James Lu,Rainer Machné,Pedro Mendes,Matthew Pocock,Nicolas Rodriguez,Alice Villéger,Darren J. Wilkinson,Sarala M. Wimalaratne,Camille Laibe,Michael Hucka,Nicolas Le Novère +26 more
TL;DR: Three ontologies created specifically to address the needs of the systems biology community are described, including the Systems Biology Ontology, which provides semantic information about the model components, and the Kinetic Simulation Algorithm Ontology and the Terminology for the Description of Dynamics, which categorizes dynamical features of the simulation results and general systems behavior.
References
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Journal ArticleDOI
SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules
TL;DR: This chapter discusses the construction of Benzenoid and Coronoid Hydrocarbons through the stages of enumeration, classification, and topological properties in a number of computers used for this purpose.
Journal ArticleDOI
The Universal Protein Resource (UniProt)
Amos Marc Bairoch,Rolf Apweiler,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.
Journal ArticleDOI
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Michael Hucka,Andrew Finney,Herbert M. Sauro,Hamid Bolouri,Hamid Bolouri,John Doyle,Hiroaki Kitano,Adam P. Arkin,Benjamin Bornstein,Dennis Bray,Athel Cornish-Bowden,Autumn A. Cuellar,S. Dronov,E. D. Gilles,Martin Ginkel,V. Gor,Igor Goryanin,W. J. Hedley,T. C. Hodgman,J.-H.S. Hofmeyr,Peter Hunter,Nick Juty,J. L. Kasberger,Andreas Kremling,Ursula Kummer,N Le Novère,Leslie M. Loew,D. Lucio,Pedro Mendes,E. Minch,Eric Mjolsness,Yoichi Nakayama,Melanie R. Nelson,Poul M. F. Nielsen,T. Sakurada,James C. Schaff,Bruce E. Shapiro,Thomas S. Shimizu,H. D. Spence,Jörg Stelling,Koichi Takahashi,Masaru Tomita,John Wagner,J. Wang +43 more
TL;DR: This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Journal ArticleDOI
From genomics to chemical genomics: new developments in KEGG
Minoru Kanehisa,Susumu Goto,Masahiro Hattori,Kiyoko F. Aoki-Kinoshita,Masumi Itoh,Shuichi Kawashima,Toshiaki Katayama,Michihiro Araki,Mika Hirakawa +8 more
TL;DR: The scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules, and RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions.
Journal ArticleDOI
BRENDA, the enzyme database: updates and major new developments
Ida Schomburg,Antje Chang,Christian Ebeling,Marion Gremse,Christian Heldt,Gregor Huhn,Dietmar Schomburg +6 more
TL;DR: BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature, that contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers.
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