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Outlier concepts auditing methodology for a large family of biomedical ontologies

机译:异常值概念为大型生物医学本体审计方法

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摘要

Abstract Background Summarization networks are compact summaries of ontologies. The “Big Picture” view offered by summarization networks enables to identify sets of concepts that are more likely to have errors than control concepts. For ontologies that have outgoing lateral relationships, we have developed the "partial-area taxonomy" summarization network. Prior research has identified one kind of outlier concepts, concepts of small partials-areas within partial-area taxonomies. Previously we have shown that the small partial-area technique works successfully for four ontologies (or their hierarchies). Methods To improve the Quality Assurance (QA) scalability, a family-based QA framework, where one QA technique is potentially applicable to a whole family of ontologies with similar structural features, was developed. The 373 ontologies hosted at the NCBO BioPortal in 2015 were classified into a collection of families based on structural features. A meta-ontology represents this family collection, including one family of ontologies having outgoing lateral relationships. The process of updating the current meta-ontology is described. To conclude that one QA technique is applicable for at least half of the members for a family F, this technique should be demonstrated as successful for six out of six ontologies in F. We describe a hypothesis setting the condition required for a technique to be successful for a given ontology. The process of a study to demonstrate such success is described. This paper intends to prove the scalability of the small partial-area technique. Results We first updated the meta-ontology classifying 566 BioPortal ontologies. There were 371 ontologies in the family with outgoing lateral relationships. We demonstrated the success of the small partial-area technique for two ontology hierarchies which belong to this family, SNOMED CT’s Specimen hierarchy and NCIt’s Gene hierarchy. Together with the four previous ontologies from the same family, we fulfilled the “six out of six” condition required to show the scalability for the whole family. Conclusions We have shown that the small partial-area technique can be potentially successful for the family of ontologies with outgoing lateral relationships in BioPortal, thus improve the scalability of this QA technique.
机译:抽象背景摘要网络是本体的紧凑概述。摘要网络提供的“大图”视图使识别比控制概念更有可能错误的概念集。对于具有外向关系的本体,我们开发了“部分地区分类”摘要网络。先前的研究已经确定了一种异常概念,部分地区分类内的小部分区域的概念。以前我们已经表明,小部分地区技术成功地为四个本体(或其层次结构)成功工作。改善质量保证(QA)可扩展性,基于家族的QA框架的方法,其中开发了一种QA技术,其中一个QA技术可能适用于具有相似结构特征的全套本体。 2015年在NCBO Bioportal举办的373个本体分类为基于结构特征的家庭集合。 Meta-Ontogology代表这个家庭集合,包括一个具有外向关系的一家人的本体。描述了更新当前元本体学的过程。为了得出结论,一个QA技术适用于家族F的至少一半成员,应该证明在F中的六个本体中的六个中的六个成功。我们描述了一种假设设置技术成功所需的条件对于给定本体。描述了研究以证明这种成功的研究的过程。本文旨在证明小部分地区技术的可扩展性。结果我们首先更新了Meta-Ontogology分类566个生物波动本体。家庭中有371个本体在横向关系中有371个本体。我们展示了属于这个家庭的两个本体层次结构的小部分地区技术的成功,Snomed CT的标本层次结构和NCIT的基因层次结构。与来自同一家庭的四个上一家本体,我们满足了为整个家庭展示可扩展性所需的“六个”条件。结论我们已经表明,小部分地区技术对于具有生物波动中的外向横向关系的本体中,可能是潜在的成功,从而提高了这种QA技术的可扩展性。

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