SBRML：一种用于将系统生物学数据与模型相关联的标记语言。

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

机构信息

Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

出版信息

Bioinformatics. 2010 Apr 1;26(7):932-8. doi: 10.1093/bioinformatics/btq069. Epub 2010 Feb 21.

DOI:10.1093/bioinformatics/btq069

PMID:20176582

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.

AVAILABILITY AND IMPLEMENTATION

The XML Schema file for SBRML is available at http://www.comp-sys-bio.org/SBRML under the Academic Free License (AFL) v3.0.

摘要

动机

系统生物学的研究是通过实验和模型的结合来进行的。已经采用了几个数据标准来表示模型（系统生物学标记语言）和各种类型的相关实验数据（例如 FuGE 和蛋白质组学标准倡议的数据）。然而，到目前为止，还没有一种标准的方法可以将模型及其实体与相应的数据集相关联，或者反之亦然。这样的标准将提供一种表示计算模拟结果的方法，并在特定模型的上下文中构建实验数据。目标应用包括模型驱动的数据分析、参数估计以及模型模拟的共享和存档。

结果

我们提出了基于 XML 的系统生物学结果标记语言（SBRML），它将模型与多个数据集相关联。每个数据集都表示为一系列与模型变量及其对应参数值相关联的值。SBRML 提供了一种灵活的索引模型参数值的方法，支持电子表格式数据和多维数据立方。我们展示并讨论了 SBRML 在酶动力学、基因表达微阵列和各种类型的模拟结果等应用中的几个使用示例。