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A Visual Interface for Querying Heterogeneous Phylogenetic Databases

机译:用于查询异构系统数据库的可视界面

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Despite the recent growth in the number of phylogenetic databases, access to these wealth of resources remain largely tool or form-based interface driven. It is our thesis that the flexibility afforded by declarative query languages may offer the opportunity to access these repositories in a better way, and to use such a language to pose truly powerful queries in unprecedented ways. In this paper, we propose a substantially enhanced closed visual query language, called PhyQL, that can be used to query phylogenetic databases represented in a canonical form. The canonical representation presented helps capture most phylogenetic tree formats in a convenient way, and is used as the storage model for our PhyloBase database for which PhyQL serves as the query language. We have implemented a visual interface for the end users to pose PhyQL queries using visual icons, and drag and drop operations defined over them. Once a query is posed, the interface translates the visual query into a Datalog query for execution over the canonical database. Responses are returned as hyperlinks to phylogenies that can be viewed in several formats using the tree viewers supported by PhyloBase. Results cached in PhyQL buffer allows secondary querying on the computed results making it a truly powerful querying architecture.
机译:尽管系统发育数据库的数量最近有所增长,但是访问这些丰富的资源仍然主要是由工具或基于表单的界面驱动的。我们的论文认为,声明性查询语言提供的灵活性可能会提供一种以更好的方式访问这些存储库的机会,并且可以使用这种语言以前所未有的方式构成真正强大的查询。在本文中,我们提出了一种实质上增强的封闭式可视查询语言,称为PhyQL,可用于查询以规范形式表示的系统发育数据库。呈现的规范表示形式有助于以方便的方式捕获大多数系统树的格式,并用作我们的PhyloBase数据库的存储模型,其中PhyQL用作查询语言。我们为最终用户实现了可视化界面,以使用可视化图标构成PhyQL查询,并在其上定义拖放操作。提出查询后,该界面会将视觉查询转换为Datalog查询,以在规范数据库上执行。响应以系统发育的超链接形式返回,可以使用PhyloBase支持的树查看器以多种格式查看系统发育。缓存在PhyQL缓冲区中的结果允许对计算结果进行二次查询,使其成为真正强大的查询体系结构。

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