Lid
Lab
Laboratory of Biological Networks
  • 04月 12

    2019 | UVGD was published!

    http://biokb.ncpsb.org/uvgd/

    https://www.tandfonline.com/doi/abs/10.1080/09553002.2019.1609127?journalCode=irab20


    Original Articles

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

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    Pages 1172-1177 | Received 26 Oct 2018, Accepted 11 Apr 2019, Accepted author version posted online: 25 Apr 2019, Published online: 13 May 2019

    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: Ultravioletgenedatabasebiological processesliterature miningmanual curation