Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
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DOI：
10.1093/bioinformatics/19.2.241
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发表时间：
2003-01-22
期刊：
影响因子：
5.8
通讯作者：
Altman, RB
中科院分区：
文献类型：
--
作者：
Yeh, I;Karp, PD;Altman, RB
动机：功能基因组学所需的计算基础架构的关键要素是传达生物学数据和知识的共享语言。基因本体论（GO； http://www.geneontology.org）提供了概念及其属性的分类法。随着尺寸的增加，其持续的构造和维护变得更具挑战性。在本文中，我们评估了知识库管理系统（KBMS），Protege-2000，对GO的维护和开发的适用性：我们转移到2000年的Protege-2000，以评估其对GO的适用性。图形用户界面支持GO的浏览和编辑。一致性检查的工具在GO中确定了较小的矛盾，并有机会减少其代表性的冗余。蛋白质公理语言被证明可用于检查本体论一致性。及时的工具使我们能够跟踪更改。使用Protege-2000，我们测试了进行更改和扩展的能力，以完善属性的语义并对更多概念进行分类。可利用：Protege-2000中的基因本体论和相关代码位于http：//smi.stanford。 edu/projects/helix/gokbms/。 Protege-200000可从http://protege.stanford.edu.contact获得：russ.altman@stanford.edu。
Motivation: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO; http://www.geneontology.org) provides a taxonomy of concepts and their attributes for annotating gene products. As GO increases in size, its ongoing construction and maintenance becomes more challenging. In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protege-2000, to the maintenance and development of GO.Results: We transferred GO to Protege-2000 in order to evaluate its suitability for GO. The graphical user interface supported browsing and editing of GO. Tools for consistency checking identified minor inconsistencies in GO and opportunities to reduce redundancy in its representation. The Protege Axiom Language proved useful for checking ontological consistency. The PROMPT tool allowed us to track changes to GO. Using Protege-2000, we tested our ability to make changes and extensions to GO to refine the semantics of attributes and classify more concepts.Availability: Gene Ontology in Protege-2000 and the associated code are located at http://smi.stanford.edu/ projects/helix/gokbms/. Protege-2000 is available from http://protege.stanford.edu.Contact: russ.altman@stanford.edu.