ROSBASE1.0: a comprehensive database of reactive oxygen species (ROS): categorization of cell organelles, proteins,...

Area of Science:

• Biochemistry and Molecular Biology
• Bioinformatics and Computational Biology

Background:

• Reactive oxygen species (ROS) play critical roles in cellular pathophysiology and pathogenesis.
• Information regarding ROS-producing, scavenging, and regulatory proteins is fragmented across scientific literature.
• A unified resource is needed to facilitate research into ROS-related diseases and potential therapeutic strategies.

Purpose of the Study:

• To develop ROSBASE 1.0, a comprehensive secondary database for ROS protein information.
• To consolidate data on ROS protein features, taxonomy, associated diseases, and interactome networks.
• To provide a centralized resource for researchers studying ROS biology.

Main Methods:

• Data integration from PubMed, UniProt, STRING, and Google Scholar.
• Development of a secondary database, ROSBASE 1.0.
• Text-mining for ROS mechanism elucidation.
• Experimental curation of protein data.

Main Results:

• ROSBASE 1.0 contains 2494 experimentally annotated entries (UniProt IDs) and 9174 PDB entries.
• The database includes data on 2447 genes, 16 cell organelles, 395 organisms, and 218 disease entries.
• 81.5% of data were experimentally curated, and 79.2% of ROS mechanisms were elucidated via text-mining.
• Quantitative insights into ROS-scavenging versus production preferences across organisms and disease categorization based on ROS involvement were reported.

Conclusions:

• ROSBASE 1.0 is the first database to consolidate diverse ROS protein data, including interactome information.
• The database provides novel quantitative data on organismal ROS preferences and disease categorization.
• ROSBASE 1.0 serves as a valuable user guide for advancing ROS biology research and therapeutic development.