Biomedical Systems and Services Laboratory, Department of Computer Science and Mathematics (DCM), University of São Paulo (FFCLRP/USP), Brazil.
Biomedical Systems and Services Laboratory, Department of Computer Science and Mathematics (DCM), University of São Paulo (FFCLRP/USP), Brazil.
J Biomed Inform. 2018 Apr;80:14-25. doi: 10.1016/j.jbi.2018.02.015. Epub 2018 Feb 27.
A conceptual model abstractly defines a number of concepts and their relationships for the purposes of understanding and communication. Once a conceptual model is available, it can also be used as a starting point for the development of a software system. The development of conceptual models using the Unified Modeling Language (UML) facilitates the representation of modeled concepts and allows software developers to directly reuse these concepts in the design of a software system. The OBO Foundry represents the most relevant collaborative effort towards the development of ontologies in the biomedical domain. The development of UML conceptual models in the biomedical domain may benefit from the use of domain-specific semantics and notation. Further, the development of these models may also benefit from the reuse of knowledge contained in OBO ontologies. This paper investigates the support for the development of conceptual models in the biomedical domain using UML as a conceptual modeling language and using the support provided by the OBO Foundry for the development of biomedical ontologies, namely entity kind and relationship types definitions provided by the Basic Formal Ontology (BFO) and the OBO Core Relations Ontology (OBO Core), respectively. Further, the paper investigates the support for the reuse of biomedical knowledge currently available in OBOFFF ontologies in the development these conceptual models. The paper describes a UML profile for the OBO Core Relations Ontology, which basically defines a number of stereotypes to represent BFO entity kinds and OBO Core relationship types definitions. The paper also presents a support toolset consisting of a graphical editor named OBO-RO Editor, which directly supports the development of UML models using the extensions defined by our profile, and a command-line tool named OBO2UML, which directly converts an OBOFFF ontology into a UML model.
一个概念模型抽象地定义了一些概念及其关系，以便于理解和交流。一旦有了概念模型，它也可以作为开发软件系统的起点。使用统一建模语言 (UML) 开发概念模型有助于表示建模概念，并允许软件开发人员在软件系统的设计中直接重用这些概念。OBO 基金会代表了在生物医学领域开发本体的最重要的协作努力。在生物医学领域开发 UML 概念模型可能受益于使用领域特定的语义和符号。此外，这些模型的开发还可能受益于对 OBO 本体中包含的知识的重用。本文研究了使用 UML 作为概念建模语言以及使用 OBO 基金会提供的生物医学本体开发支持来开发生物医学领域概念模型的支持，即分别由基本形式本体论 (BFO) 和 OBO 核心关系本体论 (OBO Core) 提供的实体类型和关系类型定义。此外，本文还研究了在开发这些概念模型时重用 OBOFFF 本体中当前可用的生物医学知识的支持。本文描述了一个针对 OBO 核心关系本体论的 UML 概要文件，它基本上定义了一些构造型，用于表示 BFO 实体类型和 OBO Core 关系类型定义。本文还介绍了一个支持工具集，其中包括一个名为 OBO-RO Editor 的图形编辑器，它直接支持使用我们的概要文件定义的扩展来开发 UML 模型，以及一个名为 OBO2UML 的命令行工具，它直接将 OBOFFF 本体转换为 UML 模型。
