GRAPHICAL AD HOC QUERY INTERFACE FOR GENBANK

我们建议为GenBank开发一个图形化的即席查询界面。 一旦成功，基因组信息学家将能够使用该工具来 以任何他们想要的方式表达对GenBank的查询。我们会 通过扩展我们当前的工具来开发此界面，该工具目前 能够通过以下方式链接多个关系基因组数据库 允许制定分布式查询。是我们建议的核心 扩展是在以下基础上开发有限的类SQL界面 以ASN.1格式存储的GenBank数据。 拟议的图形化GenBank查询界面将包括数字 显著特性，包括架构抽象、架构语义 说明、架构组件查找和联接路径发现。 架构抽象旨在解决ASN.1的复杂性 规范通过为用户提供隐藏 ASN.1模式的中间分支和一种折叠复杂结构的方法 将架构的子分支转换为架构图中的简单节点。 图式语义解释的目的是为用户提供语义 GenBank ASN.1选定的亚组分/分支的含义(英文) 架构。模式构成发现旨在帮助用户 标识ASN.1架构中与计划查询相关的部分。 Jon Path Discovery旨在发现语义上的替代方案 链接多个子模式图以形成查询的有意义的方法。 拟议的查询界面可能是以下方面的重要工具 计算生物学家，他们不仅需要自由访问 基本的核苷酸序列数据库，但也需要连接 数据库到公共和私人相关的基因组数据库。这个 界面将使用Java Applet开发，并可下载 通过互联网。

We propose to develop a graphical ad hoc query interface for GenBank. Once successful, genome informaticists would be able to use the tool to express queries against GenBank in any manner they wish. We would develop this interface by extending our current tool, which is presently capable of interlinking multiple relational genome databases by permitting formulation of distributed queries. Central to our proposed extension is the development of a limited SQL-like interface on top of GenBank data stored in ASN.1 format. The proposed graphical GenBank query interface would include a number of salient features, including Schema Abstraction, Schema Semantics Explanation, Schema Constituent Finding, and Join Path Discovery. Schema Abstraction aims at tackling the complexity of the ASN.1 specifications by providing the user with both a means of hiding intermediate branches of ASN.1 schema and a means of collapsing complex subbranches of the schema into a simple node within the schema diagram. Schema Semantics Explanation aims at providing users with the semantic meanings (in English) of chosen subcomponents/branches of GenBank ASN.1 schema. Schema Constituent Finding aims at assisting user in identifying the portion of an ASN.1 schema relevant to a planned query. Jon Path Discovery aims at discovering alternative, semantically meaningful ways of linking multiple subschema diagrams to form a query. The proposed query interface could be an essential tool for computational biologists who not only need to freely access the essential nucleotide sequence database, but also need to tie that database to both public and private related genome databases. The interface would be developed in Java applet and would be downloable through the Internet.