Chen Tao, Li Mansheng, He Qiang, Zou Lei, Li Youhuan, Chang Cheng, Zhao Dongyan, Zhu Yunping
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, Beijing, 102206, China.
School of Software and Electrical Engineering, Swinburne University of Technology, Melbourne, Victoria, 3122, Australia.
BMC Bioinformatics. 2017 Oct 13;18(1):452. doi: 10.1186/s12859-017-1852-0.
Recent 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.
We 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.
The 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 /.
组学技术的最新进展产生了大量与肝脏相关的数据。需要一个全面且最新的肝脏相关数据源，以便生物学家能够获取最新数据。然而，当前与肝脏相关的数据源各自仅涵盖肝脏的特定部分。它们难以跟上这些数据资源中可用的肝脏相关数据的快速增长。整合多样的肝脏相关数据是一项关键但艰巨的挑战，因为这需要持续的人力投入。
我们展示了LiverWiki，这是首个基于维基的数据库，它将与肝脏相关的基因、同源基因、微阵列数据集和RNA测序数据集中的基因表达、蛋白质、蛋白质相互作用、翻译后修饰、相关通路、疾病、代谢组学数据集中鉴定出的代谢物以及文献整合到一个易于访问和搜索的资源中，用于社区驱动的共享。LiverWiki在总共141,897个内容页面中存储信息，包括19,787个与肝脏相关的基因页面、17,077个同源基因页面、50,251个与肝脏相关的蛋白质页面、36,122个基因表达页面、代谢组学数据集中鉴定出的2067个代谢物、16,366个与疾病相关的分子以及227个肝脏疾病页面。除了帮助用户在LiverWiki上进行搜索、浏览、审阅和完善内容外，LiverWiki最重要的贡献是允许社区在可见且可编辑的表格中创建和更新肝脏的生物学数据。这将新产生的数据与现有知识整合在一起。LiverWiki基于MediaWiki实现，提供了强大的扩展以支持社区贡献。
LiverWiki的主要目标是为研究社区提供全面的肝脏相关数据，并允许研究社区灵活高效地共享他们的肝脏相关数据。它还通过允许发现立即被整合和共享，而不是依赖专家策展人，实现了新发现的快速共享。该数据库可在线访问http://liverwiki.hupo.org.cn/ 。
