Integrating BioPAX pathway knowledge with SBML models
Integrating BioPAX pathway knowledge with SBML models
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DOI：
10.1049/iet-syb.2009.0007
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发表时间：
2009-09-01
影响因子：
2.3
通讯作者：
Blinov, M. L.
中科院分区：
文献类型：
--
作者：
Ruebenacker, O.;Moraru, I. I.;Blinov, M. L.
在线数据库存储了数千种分子相互作用和途径，许多建模软件工具为用户提供了创建和模拟此类相互作用的数学模型的界面。然而，两个最广泛使用的标准存储路径数据（生物学路径交换; BioPAX）和交换路径的数学模型（系统生物学标记语言; SBML）的结构和语义不同。基于简单的一对一映射的格式之间的转换（使以一种格式存在的数据以另一种格式可用）可能导致数据的丢失或失真，难以自动化，并且通常不切实际和/或错误。这严重限制了知识数据和模型的集成。在本文中，我们介绍了一种方法，这种整合的基础上的桥接格式，我们命名为系统生物学途径交换（SBPAX）暗指SBML和BioPAX。它通过与SBPAX之间的一对一映射和SBPAX数据内的操作的组合，促进了不同格式数据之间的转换。SBPAX的概念是提供一个灵活的描述，围绕基本的路径数据，基本上是所有格式的共同子集描述的过程，参与这些过程的物质和它们的位置。SBPAX可以作为来自不同格式的各种来源的分子相互作用数据以及有关其相对关系的信息的存储库，从而提供了一个平台，用于在格式之间进行转换并记录转换期间使用的假设，粘合（识别不同格式的相关元素）和合并（从多个来源创建一组连贯的数据）数据。
Online databases store thousands of molecular interactions and pathways, and numerous modelling software tools provide users with an interface to create and simulate mathematical models of such interactions. However, the two most widespread used standards for storing pathway data (biological pathway exchange; BioPAX) and for exchanging mathematical models of pathways (systems biology markup language; SBML) are structurally and semantically different. Conversion between formats (making data present in one format available in another format) based on simple one-to-one mappings may lead to loss or distortion of data, is difficult to automate, and often impractical and/or erroneous. This seriously limits the integration of knowledge data and models. In this paper we introduce an approach for such integration based on a bridging format that we named systems biology pathway exchange (SBPAX) alluding to SBML and BioPAX. It facilitates conversion between data in different formats by a combination of one-to-one mappings to and from SBPAX and operations within the SBPAX data. The concept of SBPAX is to provide a flexible description expanding around essential pathway data-basically the common subset of all formats describing processes, the substances participating in these processes and their locations. SBPAX can act as a repository for molecular interaction data from a variety of sources in different formats, and the information about their relative relationships, thus providing a platform for converting between formats and documenting assumptions used during conversion, gluing (identifying related elements across different formats) and merging (creating a coherent set of data from multiple sources) data.