Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3DB, UK.
Brief Bioinform. 2013 Nov;14(6):696-712. doi: 10.1093/bib/bbs053. Epub 2012 Sep 8.
Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and methods from diverse disciplines such as information management, knowledge representation, cognitive science, linguistics and philosophy. Depending on the desired applications in which ontologies are being applied, the evaluation of research in biomedical ontologies must follow different strategies. Here, we provide a classification of research problems in which ontologies are being applied, focusing on the use of ontologies in basic and translational research, and we demonstrate how research results in biomedical ontologies can be evaluated. The evaluation strategies depend on the desired application and measure the success of using an ontology for a particular biomedical problem. For many applications, the success can be quantified, thereby facilitating the objective evaluation and comparison of research in biomedical ontology. The objective, quantifiable comparison of research results based on scientific applications opens up the possibility for systematically improving the utility of ontologies in biomedical research.
本体在生物医学领域中已经得到广泛应用，它们是标准化术语、获取领域知识、验证数据一致性以及促进异质生物医学数据集成分析的手段。为此，生物医学本体的研究应用了来自信息管理、知识表示、认知科学、语言学和哲学等多个学科的理论和方法。根据本体在应用中所期望的应用，对生物医学本体研究的评估必须遵循不同的策略。在这里，我们对本体应用的研究问题进行了分类，重点介绍了本体在基础和转化研究中的应用，并展示了如何评估生物医学本体中的研究成果。评估策略取决于预期的应用，并衡量使用本体解决特定生物医学问题的成功程度。对于许多应用，成功是可以量化的，从而促进了对生物医学本体研究的客观评估和比较。基于科学应用的客观、可量化的研究结果比较为系统地提高本体在生物医学研究中的效用提供了可能性。
