Bergmann Frank T, Rodriguez Nicolas, Le Novère Nicolas
J Integr Bioinform. 2015 Sep 4;12(2):261. doi: 10.2390/biecoll-jib-2015-261.
Several standard formats have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. The Open Modeling EXchange format (OMEX) supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, an optional metadata file, and the files describing the model. The manifest is an XML file listing all files included in the archive and their type. The metadata file provides additional information about the archive and its content. Although any format can be used, we recommend an XML serialization of the Resource Description Framework. Together with the other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails.
已经提出了几种标准格式，可用于以一致的方式描述模型、模拟、数据或其他基本信息。这些构成了重现给定已发表科学结果所需的各种单独组件。开放建模交换格式（OMEX）支持生物学建模和模拟实验所需的所有信息的交换。一个OMEX文件是一个ZIP容器，它包括一个清单文件、一个可选的元数据文件以及描述模型的文件。清单是一个XML文件，列出存档中包含的所有文件及其类型。元数据文件提供有关存档及其内容的附加信息。虽然可以使用任何格式，但我们建议使用资源描述框架的XML序列化。与生物学网络计算建模（COMBINE）中的其他标准格式一起，OMEX是COMBINE存档的基础。COMBINE存档的内容尽可能由以COMBINE标准编码的文件组成，但可能包括由互联网媒体类型定义的其他文件。COMBINE存档通过将所有相关信息嵌入一个文件中来促进生物学建模和模拟实验的重现。一次性存储和交换所有信息也有助于构建活动日志和审计跟踪。
