LiverWiki: a wiki-based database for human liver

BMC Bioinformatics

Database

Tao Chen¹  Mansheng Li¹  Yunping Zhu¹  Cheng Chang¹  Lei Zou²  Youhuan Li²  Dongyan Zhao²  Qiang He³ 

[1] Beijing Institute of Life Omics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, 33 Life Science Park Rd, Changping District, 102206, Beijing, China;Institute of Computer Science and Technology, Peking University, No.5 Yiheyuan Road Haidian District, 100871, Beijing, China;School of Software and Electrical Engineering, Swinburne University of Technology, 3122, Melbourne, Victoria, Australia;

关键词: Wiki-based database;    Human liver;    Community-driven sharing;   

DOI  :  10.1186/s12859-017-1852-0

 received in 2016-12-21, accepted in 2017-10-02,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundRecent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. However, current liver-related data sources each cover only a specific part of the liver. It is difficult for them to keep pace with the rapid increase of liver-related data available at those data resources. Integrating diverse liver-related data is a critical yet formidable challenge, as it requires sustained human effort.ResultsWe present LiverWiki, a first wiki-based database that integrates liver-related genes, homolog genes, gene expressions in microarray datasets and RNA-Seq datasets, proteins, protein interactions, post-translational modifications, associated pathways, diseases, metabolites identified in the metabolomics datasets, and literatures into an easily accessible and searchable resource for community-driven sharing. LiverWiki houses information in a total of 141,897 content pages, including 19,787 liver-related gene pages, 17,077 homolog gene pages, 50,251 liver-related protein pages, 36,122 gene expression pages, 2067 metabolites identified in the metabolomics datasets, 16,366 disease-related molecules, and 227 liver disease pages. Other than assisting users in searching, browsing, reviewing, refining the contents on LiverWiki, the most important contribution of LiverWiki is to allow the community to create and update biological data of liver in visible and editable tables. This integrates newly produced data with existing knowledge. Implemented in mediawiki, LiverWiki provides powerful extensions to support community contributions.ConclusionsThe main goal of LiverWiki is to provide the research community with comprehensive liver-related data, as well as to allow the research community to share their liver-related data flexibly and efficiently. It also enables rapid sharing new discoveries by allowing the discoveries to be integrated and shared immediately, rather than relying on expert curators. The database is available online at http://liverwiki.hupo.org.cn/.

【 授权许可】

CC BY   
© The Author(s). 2017