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Int J Radiat Biol. 2019 May 13:1-6. doi: 10.1080/09553002.2019.1609127. [Epub ahead of print]

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

Author information

1
a State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics , Beijing , China.
2
b School of Traditional Chinese Medicine, Beijing University of Chinese Medicine , Beijing , China.
3
c Beijing Institute of Radiation Medicine , Beijing , China.

Abstract

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.

KEYWORDS:

Ultraviolet; biological processes; database; gene; literature mining; manual curation

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