OBO to UML: Support for the development of conceptual models in the biomedical domain

• Published in: Journal of biomedical informatics Vol. 80; pp. 14 - 25
• Main Authors: Waldemarin, Ricardo C., de Farias, Cléver R.G.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-04-2018
• Subjects: Biological Ontologies; Conceptual modeling; Humans; Models, Theoretical; OBO Foundry ontologies reuse; UML Profile for the OBO Core Relations Ontology; Unified Medical Language System; Unified Modeling Language; Conceptual modeling; Unified Modeling Language; UML Profile for the OBO Core Relations Ontology; OBO Foundry ontologies reuse
• ISSN: 1532-0464; 1532-0480
• DOI: 10.1016/j.jbi.2018.02.015

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•A UML Profile for the OBO Core Relations Ontology.•A graphical editor for the development UML conceptual models using the profile.•Methodological support for the OBOFFF knowledge reuse in UML.•A command-line tool to transform an OBOFFF ontology into a shareable UML model.
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.