DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases

Area of Science:

• Biochemistry
• Molecular Biology
• Genomics

Background:

• RNA molecules are essential for normal cellular function but are susceptible to oxidative damage.
• Reactive oxygen species (ROS) overproduction disrupts redox homeostasis, leading to RNA oxidation.
• Oxidized RNA can result in aberrant protein synthesis, reduced translation efficiency, and contribute to various human diseases.

Purpose of the Study:

• To develop a comprehensive online knowledgebase, DES-ROD, for exploring RNA oxidation and its association with human diseases.
• To facilitate researchers' access to processed information from extensive biomedical literature.
• To enable the investigation of relationships between RNA oxidation, cellular processes, and disease pathogenesis.

Main Methods:

• Developed DES-ROD, an online knowledgebase integrating data from 298,603 PubMed abstracts and full-text articles.
• Utilized 38 curated thematic dictionaries covering genes, proteins, pathways, Gene Ontology, mutations, RNAs, enzymes, toxins, metabolites, and diseases.
• Implemented text and data mining techniques to map concepts and identify associations within the analyzed documents.

Main Results:

• DES-ROD provides access to processed information on RNA oxidation and human diseases.
• The knowledgebase allows exploration of enriched concepts and their pairwise associations.
• Case studies demonstrate the system's utility in uncovering known and potentially novel insights into RNA oxidation and disease.

Conclusions:

• DES-ROD is the first knowledgebase of its kind, specifically focused on RNA oxidation and human diseases using text and data mining.
• The system empowers researchers to investigate the multifaceted effects of RNA oxidation and its control mechanisms.
• DES-ROD aids in understanding the fundamental role of RNA oxidation in numerous human diseases.