Salhi Adil, Essack Magbubah, Alam Tanvir, Bajic Vladan P, Ma Lina, Radovanovic Aleksandar, Marchand Benoit, Schmeier Sebastian, Zhang Zhang, Bajic Vladimir B
a King Abdullah University of Science and Technology (KAUST) , Computational Bioscience Research Center (CBRC) , Thuwal , Kingdom of Saudi Arabia.
b VINCA Institute of Nuclear Sciences , Belgrade , Republic of Serbia.
RNA Biol. 2017 Jul 3;14(7):963-971. doi: 10.1080/15476286.2017.1312243. Epub 2017 Apr 7.
Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA ( www.cbrc.kaust.edu.sa/des_ncrna ). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource.
非编码RNA（ncRNAs），特别是微小RNA（miRNAs）和长链非编码RNA（lncRNAs），在疾病中起着重要作用，并成为新的药物靶点。因此，阐明ncRNAs与细胞中其他生物医学实体之间的关系对于更好地理解ncRNA的作用至关重要，这最终可能有助于开发其在医学中的应用。为了支持ncRNA研究，并便于从大量已发表的ncRNA相关研究中检索有关miRNAs和lncRNAs的相关信息，我们开发了DES-ncRNA（www.cbrc.kaust.edu.sa/des_ncrna）。DES-ncRNA是一个知识库，包含从公共科学文献和其他公共资源中通过文本和数据挖掘获得的信息。通过来自19个特定主题词典的术语和术语对，可以探索挖掘出的信息，这些词典包括例如抗生素、毒素、药物、酶、突变、途径、人类基因和蛋白质、药物适应症和副作用、突变、疾病等。DES-ncRNA包含来自这些词典的约878,000个术语关联，其中36,222（5,373）个与miRNAs（lncRNAs）有关。我们为用户提供了几种探索有关ncRNAs信息的方法，包括关联网络的受控生成以及假设生成。我们展示了一个例子，说明DES-ncRNA如何有助于阿尔茨海默病的研究，并提出法舒地尔的潜在治疗作用。DES-ncRNA是一个强大的工具，可以单独使用或作为现有资源的补充，以支持人类ncRNA的研究。据我们所知，这是唯一一个主要通过文献挖掘专门针对人类miRNAs和lncRNAs的知识库，能够探索广泛的相关生物医学实体，这是其他任何资源都无法比拟的。
