Visualizing information across multidimensional post-genomic structured and textual databases
Visualizing information across multidimensional post-genomic structured and textual databases
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DOI：
10.1093/bioinformatics/bti210
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发表时间：
2005-04-15
期刊：
影响因子：
5.8
通讯作者：
Lussier, YA
中科院分区：
文献类型：
--
作者：
Tao, Y;Friedman, C;Lussier, YA
动机：可视化生物信息之间的关系以促进理解，对于后基因组时代的生物学研究至关重要。尽管已经开发了不同的系统来查看特定数据库的基因-表型关系，但很少有系统专门设计为将多维基因和表型信息一起可视化的通用灵活工具。我们的目标是开发一种可视化多维基因和表型信息的方法和一个统一不同生物数据库的模型，以便使用统一的界面来呈现集成的知识。结果：我们开发了一个新颖、灵活和可推广的可视化工具PhenoGenesview(PGview)，在本文中，该工具用于显示来自人类精选数据库(OMIM)的基因-表型关系，以及使用自然语言处理工具BioMedLEE的自动方法。从多个数据库获得的数据首先被集成到一个统一的结构中，然后由PGview进行组织。PGview提供了灵活的查询界面，允许对数据库中的任何所需维度进行动态选择和排序。根据用户的查询，可以使用分层可扩展树来可视化结果，这些树呈现用户根据他们的研究兴趣指定的视图。我们相信，这种方法允许用户动态组织和可视化多个维度，是一个潜在的强大和有前途的工具，应该大大促进生物学研究。
Motivation: Visualizing relationships among biological information to facilitate understanding is crucial to biological research during the post-genomic era. Although different systems have been developed to view gene-phenotype relationships for specific databases, very few have been designed specifically as a general flexible tool for visualizing multidimensional genotypic and phenotypic information together. Our goal is to develop a method for visualizing multidimensional genotypic and phenotypic information and a model that unifies different biological databases in order to present the integrated knowledge using a uniform interface.Results: We developed a novel, flexible and generalizable visualization tool, called PhenoGenesviewer (PGviewer), which in this paper was used to display gene-phenotype relationships from a human-curated database (OMIM) and from an automatic method using a Natural Language Processing tool called BioMedLEE. Data obtained from multiple databases were first integrated into a uniform structure and then organized by PGviewer. PGviewer provides a flexible query interface that allows dynamic selection and ordering of any desired dimension in the databases. Based on users' queries, results can be visualized using hierarchical expandable trees that present views specified by users according to their research interests. We believe that this method, which allows users to dynamically organize and visualize multiple dimensions, is a potentially powerful and promising tool that should substantially facilitate biological research.