Karp P D, Paley S
Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA.
J Comput Biol. 1996 Spring;3(1):191-212. doi: 10.1089/cmb.1996.3.191.
The EcoCyc system consists of a knowledge base (KB) that describes the genes and intermediary metabolism of Escherichia coli, and a graphical user interface (GUI) for accessing that knowledge. This paper addresses two problems: How can we create a GUI that provides integrated access to metabolic and genomic data? We describe the design and implementation of visual presentations that closely mimic those found in the biology literature, and that offer hypertext navigation among related entities, and multiple views of the same entity. We employ a frame knowledge representation system (FRS) called HyperTHEO to manage the EcoCyc knowledge base. Among the advantages of FRSs are an expressive data model for capturing the complexities of biological information, and schema-evolution capabilities that facilitate the constant schema changes that biological databases tend to undergo. HyperTHEO also includes rule-based inference facilities that are the foundation of expert systems, a constraint language for maintaining data integrity, and a declarative query language. A graphic KB editor and browser allow the EcoCyc developers to interactively inspect and modify this evolving KB.
EcoCyc系统由一个描述大肠杆菌基因和中间代谢的知识库（KB）以及一个用于访问该知识的图形用户界面（GUI）组成。本文解决了两个问题：我们如何创建一个能够提供对代谢和基因组数据进行集成访问的GUI？我们描述了视觉呈现的设计与实现，这些呈现紧密模仿生物学文献中的呈现，并在相关实体之间提供超文本导航以及同一实体的多种视图。我们采用一种名为HyperTHEO的框架知识表示系统（FRS）来管理EcoCyc知识库。FRS的优点包括用于捕获生物信息复杂性的富有表现力的数据模型，以及有助于生物数据库往往会经历的不断模式变化的模式演化能力。HyperTHEO还包括作为专家系统基础的基于规则的推理工具、用于维护数据完整性的约束语言以及声明性查询语言。一个图形知识库编辑器和浏览器允许EcoCyc开发人员交互式地检查和修改这个不断发展的知识库。
