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SBRML: a markup language for associating systems biology data with models

Dada, Joseph O., Spasic, Irena, Paton, Norman W. and Mendes, Pedro 2010. SBRML: a markup language for associating systems biology data with models. Bioinformatics 26 (7) , pp. 932-938. 10.1093/bioinformatics/btq069

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Abstract

MOTIVATION: Research in systems biology is carried out through a combination of experiments and models. Several data standards have been adopted for representing models (Systems Biology Markup Language) and various types of relevant experimental data (such as FuGE and those of the Proteomics Standards Initiative). However, until now, there has been no standard way to associate a model and its entities to the corresponding datasets, or vice versa. Such a standard would provide a means to represent computational simulation results as well as to frame experimental data in the context of a particular model. Target applications include model-driven data analysis, parameter estimation, and sharing and archiving model simulations. RESULTS: We propose the Systems Biology Results Markup Language (SBRML), an XML-based language that associates a model with several datasets. Each dataset is represented as a series of values associated with model variables, and their corresponding parameter values. SBRML provides a flexible way of indexing the results to model parameter values, which supports both spreadsheet-like data and multidimensional data cubes. We present and discuss several examples of SBRML usage in applications such as enzyme kinetics, microarray gene expression and various types of simulation results.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Computer Science & Informatics
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Q Science > QH Natural history > QH301 Biology
Uncontrolled Keywords: Spasic; Systems biology results markup language
Publisher: Oxford University Press
ISSN: 1460-2059
Last Modified: 15 Nov 2013 09:25
URI: http://orca-mwe.cf.ac.uk/id/eprint/6205

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