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UMLS Semantic Network as a UML Metamodel for Improving Biomedical Ontology and Application Modeling

机译:UMLS语义网络作为用于改善生物医学本体和应用程序建模的UML元模型

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摘要

In the domain of biomedical and health informatics, ontologies are widely used to capture knowledge ranging from bioinformatics such as gene, protein, protein interactions, etc. to clinical/healthcare informatics knowledge such as diseases, symptoms, treatment, medication, etc. Currently, one medical knowledge source that encapsulates a broad spectrum of medical knowledge is the Unified Medical Language System (UMLS), which can be defined as a compendium of diverse medical ontological standards. The primary components of the UMLS are: Semantic Network (UMLS-SN) - designed by interconnecting well-defined semantic types with semantic relationships, and Metathesaurus (UMLS-META) - the base of UMLS system that is comprised of millions of medical concepts from diverse medical standards. However, within the biomedical and health informatics community, the concepts of software engineering and domain modeling (using meta-models such as ERD, UML, and XML) are very successful in designing and implementing biomedical/health domain application models. In the current status, the UMLS-SN is primarily employed for classification of medical concepts in UMLS-META, but UMLS-SN knowledge can't be viewed or employed as a modeling framework for designing ontological models and is restricted to the UMLS environment. Thus, the impact of the biomedical semantics captured by UMLS-SN might be minimal in medical facilities, research and healthcare organizations that are highly influenced by software engineering, meta-models and domain model-based practices. In order fill this gap, the authors propose a meta-modeling framework for UMLS-SN based on the UML Profile (built using UML meta-model) that will result in a customized domain specific meta-model. This specialized metamodel that encapsulates the medical knowledge semantics of UMLS-SN can then be employed for designing ontological models or relevant healthcare application models and simultaneously be coherent with software meta-models and domain modeling practices.
机译:在生物医学和健康信息学领域,本体被广泛用于捕获从基因,蛋白质,蛋白质相互作用等生物信息学到疾病,症状,治疗,药物等临床/保健信息学知识的知识。目前,涵盖广泛医学知识的医学知识来源之一是统一医学语言系统(UMLS),可以将其定义为各种医学本体论标准的纲要。 UMLS的主要组件是:语义网络(UMLS-SN)-通过将定义良好的语义类型与语义关系互连而设计;以及Metathesaurus(UMLS-META)-UMLS系统的基础,该系统由数百万个医学概念组成多种医疗标准。但是,在生物医学和健康信息学界,软件工程和领域建模(使用诸如ERD,UML和XML等元模型的领域)的概念在设计和实现生物医学/健康领域应用程序模型方面非常成功。在当前状态下,UMLS-SN主要用于UMLS-META中医学概念的分类,但是UMLS-SN知识不能被视为或用作设计本体模型的建模框架,并且仅限于UMLS环境。因此,由UMLS-SN捕获的生物医学语义的影响在受软件工程,元模型和基于域模型的实践高度影响的医疗机构,研究和医疗机构中可能很小。为了填补这一空白,作者提出了一个基于UML概要文件(使用UML元模型构建)的UMLS-SN元模型框架,该框架将产生定制的领域特定元模型。然后,可以将封装UMLS-SN的医学知识语义的专用元模型用于设计本体模型或相关的医疗应用程序模型,并同时与软件元模型和域建模实践保持一致。

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