MOTIVATION Biomolecular data stored in public databases is increasingly specialized to organisms, context/pathology and tissue type, potentially resulting in significant overhead for analyses. These networks are often specializations of generic interaction sets, presenting opportunities for reducing storage and computational cost. Therefore, it is desirable to develop effective compression and storage techniques, along with efficient algorithms and a flexible query interface capable of operating on compressed data structures. Current graph databases offer varying levels of support for network integration. However, these solutions do not provide efficient methods for the storage and querying of versioned networks. RESULTS We present VerTIoN, a framework consisting of novel data structures and associated query mechanisms for integrated querying of versioned context-specific biological networks. As a use case for our framework, we study network proximity queries in which the user can select and compose a combination of tissue-specific and generic networks. Using our compressed version tree data structure, in conjunction with state-of-the-art numerical techniques, we demonstrate real-time querying of large network databases. CONCLUSION Our results show that it is possible to support flexible queries defined on heterogeneous networks composed at query time while drastically reducing response time for multiple simultaneous queries. The flexibility offered by VerTIoN in composing integrated network versions opens significant new avenues for the utilization of ever increasing volume of context-specific network data in a broad range of biomedical applications. AVAILABILITY AND IMPLEMENTATION VerTIoN is implemented as a C++ library and is available at http://compbio.case.edu/omics/software/vertion and https://github.com/tjcowman/vertion. CONTACT tyler.cowman@case.edu.

中文翻译：

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特定于上下文的生物网络的集成查询和版本控制。


动机存储在公共数据库中的生物分子数据越来越专门针对生物体、背景/病理学和组织类型，这可能会导致巨大的分析开销。这些网络通常是通用交互集的专门化，提供了降低存储和计算成本的机会。因此，需要开发有效的压缩和存储技术，以及能够对压缩数据结构进行操作的高效算法和灵活的查询接口。当前的图形数据库为网络集成提供不同级别的支持。然而，这些解决方案没有提供用于版本化网络的存储和查询的有效方法。结果我们提出了 VerTIoN，一个由新颖的数据结构和相关查询机制组成的框架，用于集成查询版本化的上下文特定生物网络。作为我们框架的一个用例，我们研究网络邻近查询，用户可以在其中选择并组成组织特定网络和通用网络的组合。使用我们的压缩版本树数据结构，结合最先进的数值技术，我们演示了大型网络数据库的实时查询。结论我们的结果表明，可以支持在查询时组成的异构网络上定义的灵活查询，同时大大减少多个同时查询的响应时间。 VerTIoN 在构建集成网络版本方面提供的灵活性为在广泛的生物医学应用中利用不断增加的上下文特定网络数据量开辟了重要的新途径。可用性和实现 VerTIoN 作为 C++ 库实现，可从 http://compbio.case 获取。edu/omics/software/version 和 https://github.com/tjcowman/version。联系 tyler.cowman@case.edu。