UVGD 1.0: a gene-centric database bridging ultraviolet radiation and molecular biology effects in organisms

Objectives: Exposing to ultraviolet for a certain time will trigger some significant molecular biology effects in an organism. In the past few decades, varied ultraviolet-associated biological effects as well as their related genes, have been discovered under biologists' efforts. However, information about ultraviolet-related genes is dispersed in thousands of scientific papers, and there is still no study emphasizing on the systematic collection of ultraviolet-related genes. Methods: We collected ultraviolet-related genes and built this gene-centric database UVGD based on literature mining and manual curation. Literature mining was based on the ultraviolet-related abstracts downloaded from PubMed, and we obtained sentences in which ultraviolet keywords and genes co-occur at single-sentence level by using bio-entity recognizer. After that, manual curation was implemented in order to identify whether the genes are related to ultraviolet or not. Results: We built the ultraviolet-related knowledge base UVGD 1.0 (URL: http://biokb.ncpsb.org/UVGD/ ), which contains 663 ultraviolet-related genes, together with 17 associated biological processes, 117 associated phenotypes, and 2628 MeSH terms. Conclusion: UVGD is helpful to understand the ultraviolet-related biological processes in organisms and we believe it would be useful for biologists to study the responding mechanisms to ultraviolet.