Department of Computer Science,University of Verona, Strada Le Grazie, Verona, Italy.
Institute for Biomedical Technologies, National Research Council (CNR), Bari, Italy.
BMC Bioinformatics. 2018 Oct 15;19(Suppl 10):350. doi: 10.1186/s12859-018-2298-8.
High throughput technologies have provided the scientific community an unprecedented opportunity for large-scale analysis of genomes. Non-coding RNAs (ncRNAs), for a long time believed to be non-functional, are emerging as one of the most important and large family of gene regulators and key elements for genome maintenance. Functional studies have been able to assign to ncRNAs a wide spectrum of functions in primary biological processes, and for this reason they are assuming a growing importance as a potential new family of cancer therapeutic targets. Nevertheless, the number of functionally characterized ncRNAs is still too poor if compared to the number of new discovered ncRNAs. Thus platforms able to merge information from available resources addressing data integration issues are necessary and still insufficient to elucidate ncRNAs biological roles.
In this paper, we describe a platform called Arena-Idb for the retrieval of comprehensive and non-redundant annotated ncRNAs interactions. Arena-Idb provides a framework for network reconstruction of ncRNA heterogeneous interactions (i.e., with other type of molecules) and relationships with human diseases which guide the integration of data, extracted from different sources, via mapping of entities and minimization of ambiguity.
Arena-Idb provides a schema and a visualization system to integrate ncRNA interactions that assists in discovering ncRNA functions through the extraction of heterogeneous interaction networks. The Arena-Idb is available at http://arenaidb.ba.itb.cnr.it.
高通量技术为科学界提供了一个前所未有的机会，可大规模分析基因组。长期以来被认为是非功能性的非编码 RNA（ncRNA），正在成为最重要和最大的基因调控因子家族之一，也是基因组维持的关键要素。功能研究已经能够将 ncRNA 分配到初级生物过程中的广泛功能，因此，它们作为潜在的新癌症治疗靶标家族的重要性日益增加。然而，如果与新发现的 ncRNA 数量相比，功能表征的 ncRNA 数量仍然太少。因此，需要能够合并来自解决数据集成问题的可用资源的信息的平台，并且仍然不足以阐明 ncRNA 的生物学作用。
在本文中，我们描述了一个名为 Arena-Idb 的平台，用于检索全面且非冗余注释的 ncRNA 相互作用。Arena-Idb 提供了一个框架，用于重构 ncRNA 异质相互作用（即与其他类型的分子）的网络以及与人类疾病的关系，该框架通过实体映射和最小化歧义来指导数据的整合，这些数据来自不同的来源。
Arena-Idb 提供了一个模式和可视化系统来整合 ncRNA 相互作用，通过提取异质相互作用网络，有助于发现 ncRNA 的功能。Arena-Idb 可在 http://arenaidb.ba.itb.cnr.it 上获得。
