Lawrence Berkeley National Laboratory, Mail Stop 64R0121, Berkeley, CA 94720, USA.
J Biomed Inform. 2011 Feb;44(1):80-6. doi: 10.1016/j.jbi.2010.02.002. Epub 2010 Feb 10.
The Gene Ontology (GO) consists of nearly 30,000 classes for describing the activities and locations of gene products. Manual maintenance of ontology of this size is a considerable effort, and errors and inconsistencies inevitably arise. Reasoners can be used to assist with ontology development, automatically placing classes in a subsumption hierarchy based on their properties. However, the historic lack of computable definitions within the GO has prevented the user of these tools. In this paper, we present preliminary results of an ongoing effort to normalize the GO by explicitly stating the definitions of compositional classes in a form that can be used by reasoners. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry candidate ontologies for chemical entities, proteins, biological qualities and anatomical entities. Using these logical definitions we are gradually beginning to automate many aspects of ontology development, detecting errors and filling in missing relationships. These definitions also enhance the GO by weaving it into the fabric of a wider collection of interoperating ontologies, increasing opportunities for data integration and enhancing genomic analyses.
GO 包含近 30000 个类，用于描述基因产物的活动和位置。手动维护如此规模的本体是一项相当大的工作，不可避免地会出现错误和不一致。推理机可用于辅助本体开发，根据其属性自动将类置于包含层次结构中。然而，GO 中历史上缺乏可计算的定义，阻止了这些工具的用户使用。在本文中，我们介绍了正在进行的一项工作的初步结果，该工作通过以可被推理机使用的形式明确陈述组合类的定义来对 GO 进行规范化。这些定义被划分为相互排斥的叉积集，其中许多集引用了其他 OBO 基金会候选化学实体、蛋白质、生物质量和解剖实体本体。使用这些逻辑定义，我们逐渐开始自动化本体开发的许多方面，检测错误并填补缺失的关系。这些定义还通过将 GO 编织到更广泛的互操作本体集合中，增加了数据集成的机会并增强了基因组分析。
