Previde Paul, Thomas Brook, Wong Mike, Mallory Emily K, Petkovic Dragutin, Altman Russ B, Kulkarni Anagha
Department of Computer Science, San Francisco State University, San Francisco, California 94132, U.S.A.,
Pac Symp Biocomput. 2018;23:590-601.
Obtaining relevant information about gene interactions is critical for understanding disease processes and treatment. With the rise in text mining approaches, the volume of such biomedical data is rapidly increasing, thereby creating a new problem for the users of this data: information overload. A tool for efficient querying and visualization of biomedical data that helps researchers understand the underlying biological mechanisms for diseases and drug responses, and ultimately helps patients, is sorely needed. To this end we have developed GeneDive, a web-based information retrieval, filtering, and visualization tool for large volumes of gene interaction data. GeneDive offers various features and modalities that guide the user through the search process to efficiently reach the information of their interest. GeneDive currently processes over three million gene-gene interactions with response times within a few seconds. For over half of the curated gene sets sourced from four prominent databases, more than 80% of the gene set members are recovered by GeneDive. In the near future, GeneDive will seamlessly accommodate other interaction types, such as gene-drug and gene-disease interactions, thus enabling full exploration of topics such as precision medicine. The GeneDive application and information about its underlying system architecture are available at http://www.genedive.net.
获取有关基因相互作用的相关信息对于理解疾病过程和治疗至关重要。随着文本挖掘方法的兴起，此类生物医学数据的数量正在迅速增加，从而给这些数据的用户带来了一个新问题：信息过载。迫切需要一种能够高效查询和可视化生物医学数据的工具，以帮助研究人员理解疾病和药物反应的潜在生物学机制，并最终造福患者。为此，我们开发了GeneDive，这是一种基于网络的信息检索、过滤和可视化工具，用于处理大量基因相互作用数据。GeneDive提供了各种功能和模式，引导用户完成搜索过程，以高效获取他们感兴趣的信息。GeneDive目前可处理超过三百万个基因-基因相互作用，响应时间在几秒内。对于从四个著名数据库获取的超过一半的精选基因集，GeneDive能够找回其中超过80%的基因集成员。在不久的将来，GeneDive将无缝纳入其他相互作用类型，如基因-药物和基因-疾病相互作用，从而能够全面探索诸如精准医学等主题。GeneDive应用程序及其底层系统架构的相关信息可在http://www.genedive.net上获取。
