Strömbäck Lena, Hall David, Lambrix Patrick
Department of Computer and Information Science, Linköpings Universitet, Linköping, Sweden.
Proteomics. 2007 Mar;7(6):857-67. doi: 10.1002/pmic.200600438.
The rapid increase in experimental data within systems biology has increased the need for exchange of data to allow analysis and comparison of larger datasets. This has resulted in a need for standardized formats for representation of such results and currently many formats for representation of data have been developed or are under development. In this paper, we give an overview of the current state of available standards and ontologies within systems biology. We focus on XML-based standards for exchange of data and give a thorough description of similarities and differences of currently available formats. For each of these, we discuss how the important concepts such as substances, interactions, and experimental data can be represented. In particular, we note that the purpose of a standard is often visible in the structures it provides for the representation of data. A clear purpose is also crucial for the success of a standard. Moreover, we note that the development of representation formats is parallel to the development of ontologies and the recent trend is that representation formats make more and more use of available ontologies.
系统生物学中实验数据的快速增长，使得对数据交换的需求增加，以便能够分析和比较更大的数据集。这就产生了对表示此类结果的标准化格式的需求，目前已经开发或正在开发许多数据表示格式。在本文中，我们概述了系统生物学中现有标准和本体的当前状态。我们重点关注基于XML的数据交换标准，并详细描述当前可用格式的异同。对于每种格式，我们讨论如何表示诸如物质、相互作用和实验数据等重要概念。特别是，我们注意到标准的目的通常在其为数据表示提供的结构中可见。明确的目的对于标准的成功也至关重要。此外，我们注意到表示格式的发展与本体的发展并行，最近的趋势是表示格式越来越多地使用现有的本体。
