Semantic interoperability: ontological unpacking of a viral conceptual model

BMC Bioinformatics

Research

Giancarlo Guizzardi¹  Anna Bernasconi²  Veda C. Storey³  Oscar Pastor⁴ 

[1] Conceptual and Cognitive Modeling Research Group, Free University of Bozen-Bolzano, Bolzano, Italy;Services and Cybersecurity Group, University of Twente, Enschede, The Netherlands;Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy;PROS Research Center, VRAIN Research Institute, Universitat Politècnica de València, Valencia, Spain;J. Mack Robinson College of Business, Georgia State University, Atlanta, Georgia, USA;PROS Research Center, VRAIN Research Institute, Universitat Politècnica de València, Valencia, Spain;

关键词: Ontological analysis;    Conceptual modeling;    OntoUML;    COVID-19;    SARS-CoV-2;    Viral genome;   

DOI  :  10.1186/s12859-022-05022-0

 received in 2022-10-17, accepted in 2022-10-29,  发布年份 2022

来源: Springer

【 摘 要 】

BackgroundGenomics and virology are unquestionably important, but complex, domains being investigated by a large number of scientists. The need to facilitate and support work within these domains requires sharing of databases, although it is often difficult to do so because of the different ways in which data is represented across the databases. To foster semantic interoperability, models are needed that provide a deep understanding and interpretation of the concepts in a domain, so that the data can be consistently interpreted among researchers.ResultsIn this research, we propose the use of conceptual models to support semantic interoperability among databases and assess their ontological clarity to support their effective use. This modeling effort is illustrated by its application to the Viral Conceptual Model (VCM) that captures and represents the sequencing of viruses, inspired by the need to understand the genomic aspects of the virus responsible for COVID-19. For achieving semantic clarity on the VCM, we leverage the “ontological unpacking” method, a process of ontological analysis that reveals the ontological foundation of the information that is represented in a conceptual model. This is accomplished by applying the stereotypes of the OntoUML ontology-driven conceptual modeling language.As a result, we propose a new OntoVCM, an ontologically grounded model, based on the initial VCM, but with guaranteed interoperability among the data sources that employ it.ConclusionsWe propose and illustrate how the unpacking of the Viral Conceptual Model resolves several issues related to semantic interoperability, the importance of which is recognized by the “I” in FAIR principles. The research addresses conceptual uncertainty within the domain of SARS-CoV-2 data and knowledge.The method employed provides the basis for further analyses of complex models currently used in life science applications, but lacking ontological grounding, subsequently hindering the interoperability needed for scientists to progress their research.

【 授权许可】

CC BY   
© The Author(s) 2022

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