Alignment of the UMLS semantic network with BioTop: methodology and assessment.
Alignment of the UMLS semantic network with BioTop: methodology and assessment.
复制标题
DOI：
10.1093/bioinformatics/btp194
复制
发表时间：
2009-06-15
期刊：
影响因子：
--
通讯作者：
van Mulligen EM
中科院分区：
文献类型：
--
作者：
Schulz S;Beisswanger E;van den Hoek L;Bodenreider O;van Mulligen EM
动机：多年来，统一医学语言系统（UMLS）的语义网络（SN）已被用作一个上层的语义框架，用于生物医学术语资源的术语分类。BioTop最近被开发为生物医学领域的上层本体。与SN相比，它建立在严格的本体论原则之上，使用OWL DL作为正式的表示语言，这已经成为语义Web的标准。为了使基于逻辑的推理与SN注释或分类的资源，映射本体的开发对齐SN与BioTop。研究方法：的理论基础和实际实现的对齐进行了描述，重点是设计决策，遇到的问题和适应的BioTop，成为必要的。为了评估的目的，UMLS概念对获得的MEDLINE摘要命名实体识别系统进行了测试可能的语义关系。此外，检查UMLS元词库中出现的所有语义类型组合的可满足性。结果如下：这个费力的比对过程需要对BioTop进行重大的设计变更和增强，并带来了几个可以修复的设计错误。人类策展人和本体之间的比较只产生了很低的一致性。本体推理也被用来成功地识别133个不一致的语义类型组合。可用性：BioTop、UMLS SN的OWL DL表示和映射本体可在http://www.purl.org/biotop/上获得。联系方式：stschulz@uni-freiburg.de
Motivation: For many years, the Unified Medical Language System (UMLS) semantic network (SN) has been used as an upper-level semantic framework for the categorization of terms from terminological resources in biomedicine. BioTop has recently been developed as an upper-level ontology for the biomedical domain. In contrast to the SN, it is founded upon strict ontological principles, using OWL DL as a formal representation language, which has become standard in the semantic Web. In order to make logic-based reasoning available for the resources annotated or categorized with the SN, a mapping ontology was developed aligning the SN with BioTop. Methods: The theoretical foundations and the practical realization of the alignment are being described, with a focus on the design decisions taken, the problems encountered and the adaptations of BioTop that became necessary. For evaluation purposes, UMLS concept pairs obtained from MEDLINE abstracts by a named entity recognition system were tested for possible semantic relationships. Furthermore, all semantic-type combinations that occur in the UMLS Metathesaurus were checked for satisfiability. Results: The effort-intensive alignment process required major design changes and enhancements of BioTop and brought up several design errors that could be fixed. A comparison between a human curator and the ontology yielded only a low agreement. Ontology reasoning was also used to successfully identify 133 inconsistent semantic-type combinations. Availability: BioTop, the OWL DL representation of the UMLS SN, and the mapping ontology are available at http://www.purl.org/biotop/. Contact: stschulz@uni-freiburg.de
登录
查看更多内容
生物医学领域的高级本体论。
影响因子：
--
作者：
McCray, AT
通讯作者：
McCray, AT
影响因子：
5.8
作者：
Jelier, R;Jenster, G;Kors, JA
通讯作者：
Kors, JA
影响因子：
2.5
作者：
Golbreich, Christine;Zhang, Songmao;Bodenreider, Olivier
通讯作者：
Bodenreider, Olivier
影响因子：
3
作者：
Berners-Lee, T;Hendler, J;Lassila, O
通讯作者：
Lassila, O
影响因子：
1
作者：
Beisswanger, Elena;Schulz, Stefan;Hahn, Udo
通讯作者：
Hahn, Udo