SBRML- A Markup Language for Encoding Systems Biology Results

Abstract

Abstract Background: The wide acceptance of Systems Biology Markup Language (SBML) as standard format for models of biochemical systems makes it possible to build, share, evaluate and develop biochemical models cooperatively. However, there is currently no standard format for encoding the results of computational analyses of systems biology models. To address this issue, we present here the Systems Biology Results Markup Language (SBRML), an XML-based format for representing systems biology results. SBRML provides a means of representing computational simulation results as well as encoding experimental data in the context of a particular model. Methods & Results: SBRML is based on XML and is specified through the XML Schema language. SBRML Object Model (SBRML-OM) was first developed using the Universal Modelling Language (UML), and a Model-Driven Architecture (MDA) approach was then used to derive the corresponding XML Schema semi-automatically with the help of mapping rules for classes and associations. SBRML can be used to describe any type of systems biology results, the model that is used to generate the results, the ontology terms that link all the terms/vocabularies used to an external ontology sources, the operation (e.g. time course, steady state etc.) that is performed on the model and a flexible means for encoding the results of the operation. SBRML associates a model with several data sets. Each data set consists of a series of values associated with model variables, and their corresponding parameter values. It provides a flexible way of indexing both simulation results and experimental data to model parameter values which supports both spreadsheet-like data or multidimensional data cubes. Some of its major uses are: associating experimental results with models for passing to analysis tools, sharing and archiving of model simulations and recording the results of analysis for validation, archiving or comparison. Conclusions: SBRML is a software-neutral language intended to allow any type of systems biology results to be represented. Standardization of systems biology results format will bring obvious benefits in terms of storage and retrieval, but will also benefit any program that needs to read data in the context of a biochemical model. Application areas are enzyme kinetics data, microarray gene expression data, and various types of simulation results. We will soon release a library (in various programming languages) for reading and writing SBRML documents.