Disjunctive shared information between ontology concepts: application to Gene Ontology.
Disjunctive shared information between ontology concepts: application to Gene Ontology.
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DOI：
10.1186/2041-1480-2-5
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发表时间：
2011-08-31
影响因子：
1.9
通讯作者：
Silva MJ
中科院分区：
文献类型：
--
作者：
Couto FM;Silva MJ
大规模的努力，在开发，维护和生物医学本体可用的激励应用相似性措施，比较本体概念，或通过扩展，其中描述的实体。一种常见的方法，称为语义相似性，通过它们在本体中共享的信息内容来比较本体概念。然而，本体中不同的析取祖先经常被忽略，或没有适当地探索，语义相似性的措施。本文提出了一种新的方法，称为DiShIn，有效地利用了许多生物医学本体中存在的多重继承关系。DiShIn计算两个本体概念的共享信息内容，基于被比较的概念的析取共同祖先的信息内容。DiShin通过从概念到其共同祖先的不同路径的数量来识别这些分离的祖先。DiShIn应用于基因本体论，并使用CESSM（一种公开可用的蛋白质相似性度量评估平台）对最先进的度量评估其性能。通过修改传统的语义相似性度量计算共享信息内容的方式，DiShIn能够获得语义和序列相似性之间的统计学显着更高的相关性。此外，在利用多重继承的现有应用程序中合并DiShIn将减少其执行时间。
The large-scale effort in developing, maintaining and making biomedical ontologies available motivates the application of similarity measures to compare ontology concepts or, by extension, the entities described therein. A common approach, known as semantic similarity, compares ontology concepts through the information content they share in the ontology. However, different disjunctive ancestors in the ontology are frequently neglected, or not properly explored, by semantic similarity measures. This paper proposes a novel method, dubbed DiShIn, that effectively exploits the multiple inheritance relationships present in many biomedical ontologies. DiShIn calculates the shared information content of two ontology concepts, based on the information content of the disjunctive common ancestors of the concepts being compared. DiShIn identifies these disjunctive ancestors through the number of distinct paths from the concepts to their common ancestors. DiShIn was applied to Gene Ontology and its performance was evaluated against state-of-the-art measures using CESSM, a publicly available evaluation platform of protein similarity measures. By modifying the way traditional semantic similarity measures calculate the shared information content, DiShIn was able to obtain a statistically significant higher correlation between semantic and sequence similarity. Moreover, the incorporation of DiShIn in existing applications that exploit multiple inheritance would reduce their execution time.
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