Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
Laboratory of Radiobiology and Molecular Genetics, Institute of Nuclear Sciences Vinca, University of Belgrade, Mike Petrovica Alasa 12-14, 11000 Belgrade, Serbia.
Oxid Med Cell Longev. 2020 Mar 27;2020:5904315. doi: 10.1155/2020/5904315. eCollection 2020.
Normal cellular physiology and biochemical processes require undamaged RNA molecules. However, RNAs are frequently subjected to oxidative damage. Overproduction of reactive oxygen species (ROS) leads to RNA oxidation and disturbs redox (oxidation-reduction reaction) homeostasis. When oxidation damage affects RNA carrying protein-coding information, this may result in the synthesis of aberrant proteins as well as a lower efficiency of translation. Both of these, as well as imbalanced redox homeostasis, may lead to numerous human diseases. The number of studies on the effects of RNA oxidative damage in mammals is increasing by year due to the understanding that this oxidation fundamentally leads to numerous human diseases. To enable researchers in this field to explore information relevant to RNA oxidation and effects on human diseases, we developed DES-ROD, an online knowledgebase that contains processed information from 298,603 relevant documents that consist of PubMed abstracts and PubMed Central full-text articles. The system utilizes concepts/terms from 38 curated thematic dictionaries mapped to the analyzed documents. Researchers can explore enriched concepts, as well as enriched pairs of putatively associated concepts. In this way, one can explore mutual relationships between any combinations of two concepts from used dictionaries. Dictionaries cover a wide range of biomedical topics, such as human genes and proteins, pathways, Gene Ontology categories, mutations, noncoding RNAs, enzymes, toxins, metabolites, and diseases. This makes insights into different facets of the effects of RNA oxidation and the control of this process possible. The usefulness of the DES-ROD system is demonstrated by case studies on some known information, as well as potentially novel information involving RNA oxidation and diseases. DES-ROD is the first knowledgebase based on text and data mining that focused on the exploration of RNA oxidation and human diseases.
正常的细胞生理和生化过程需要未受损的 RNA 分子。然而，RNA 经常受到氧化损伤。活性氧（ROS）的过度产生导致 RNA 氧化，并扰乱氧化还原（氧化还原反应）平衡。当氧化损伤影响携带蛋白质编码信息的 RNA 时，这可能导致异常蛋白质的合成以及翻译效率降低。这两者以及氧化还原平衡的失衡，可能导致许多人类疾病。由于理解到这种氧化从根本上导致了许多人类疾病，因此，研究哺乳动物中 RNA 氧化损伤影响的研究逐年增加。为了使该领域的研究人员能够探索与 RNA 氧化和对人类疾病的影响相关的信息，我们开发了 DES-ROD，这是一个在线知识库，其中包含来自 298,603 篇相关文献的处理信息，这些文献包括 PubMed 摘要和 PubMed Central 全文文章。该系统利用从 38 个经过策展的主题词典中提取的概念/术语来映射到分析的文档。研究人员可以探索丰富的概念，以及丰富的潜在关联概念对。通过这种方式，可以探索使用的词典中任意两个概念之间的相互关系。词典涵盖了广泛的生物医学主题，如人类基因和蛋白质、途径、GO 类别、突变、非编码 RNA、酶、毒素、代谢物和疾病。这使得深入了解 RNA 氧化的影响和对该过程的控制的不同方面成为可能。通过对一些已知信息和涉及 RNA 氧化和疾病的潜在新信息的案例研究，证明了 DES-ROD 系统的有用性。DES-ROD 是第一个基于文本和数据挖掘的知识库，专注于探索 RNA 氧化和人类疾病。
