Scharm Martin, Waltemath Dagmar, Mendes Pedro, Wolkenhauer Olaf
Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
School of Computer Science and Manchester Institute of Biotechnology, University of Manchester, Manchester, Great Britain.
J Biomed Semantics. 2016 Jul 11;7(1):46. doi: 10.1186/s13326-016-0080-2.
Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to different model versions. Taken together, the underlying changes reflect a model's provenance and thus can give valuable insights into the studied biology. Currently, however, changes cannot be semantically interpreted. To improve this situation, we developed an ontology of terms describing changes in models. The ontology can be used by scientists and within software to characterise model updates at the level of single changes. When studying or reusing a model, these annotations help with determining the relevance of a change in a given context.
We manually studied changes in selected models from BioModels and the Physiome Model Repository. Using the BiVeS tool for difference detection, we then performed an automatic analysis of changes in all models published in these repositories. The resulting set of concepts led us to define candidate terms for the ontology. In a final step, we aggregated and classified these terms and built the first version of the ontology.
We present COMODI, an ontology needed because COmputational MOdels DIffer. It empowers users and software to describe changes in a model on the semantic level. COMODI also enables software to implement user-specific filter options for the display of model changes. Finally, COMODI is a step towards predicting how a change in a model influences the simulation results.
COMODI, coupled with our algorithm for difference detection, ensures the transparency of a model's evolution, and it enhances the traceability of updates and error corrections. COMODI is encoded in OWL. It is openly available at http://comodi.sems.uni-rostock.de/ .
开放模型存储库提供了可直接复用的生物系统计算模型。这些存储库中的模型会随着时间不断演变，从而产生不同的模型版本。总体而言，这些潜在的变化反映了模型的出处，因此能够为所研究的生物学提供有价值的见解。然而，目前这些变化无法进行语义解释。为改善这种情况，我们开发了一个用于描述模型变化的术语本体。科学家和软件可以使用该本体在单个变化层面上对模型更新进行特征描述。在研究或复用模型时，这些注释有助于确定给定背景下变化的相关性。
我们手动研究了来自生物模型库（BioModels）和生理组模型存储库中选定模型的变化。然后使用差异检测工具BiVeS对这些存储库中发布的所有模型的变化进行自动分析。由此得到的概念集引导我们定义本体的候选术语。在最后一步，我们对这些术语进行汇总和分类，并构建了本体的第一个版本。
我们提出了COMODI，这是一个因计算模型存在差异而需要的本体。它使用户和软件能够在语义层面描述模型的变化。COMODI还使软件能够实现用户特定的过滤器选项，用于显示模型变化。最后，COMODI朝着预测模型中的变化如何影响模拟结果迈出了一步。
COMODI与我们的差异检测算法相结合，确保了模型演变的透明度，并增强了更新和纠错的可追溯性。COMODI以OWL编码。可在http://comodi.sems.uni-rostock.de/ 上公开获取。
