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Analyzing User Interactions with Biomedical Ontologies: A Visual Perspective

21 Pages Posted: 23 Jun 2018 First Look: Accepted

See all articles by Maulik Kamdar

Maulik Kamdar

Stanford University - Center for Biomedical Informatics Research

Simon Walk

Stanford University - Center for Biomedical Informatics Research

Tania Tudorache

Stanford University - Center for Biomedical Informatics Research

Mark Musen

Stanford University - Center for Biomedical Informatics Research

Abstract

Biomedical ontologies are large: Several ontologies in the BioPortal repository contain thousands or even hundreds of thousands of entities. The development and maintenance of such large ontologies is difficult. To support ontology authors and repository developers in their work, it is crucial to improve our understanding of how these ontologies are explored, queried, reused, and used in downstream applications by biomedical researchers. We present an exploratory empirical analysis of user activities in the BioPortal ontology repository by analyzing BioPortal interaction logs across different access modes over several years. We investigate how users of BioPortal query and search for ontologies and their classes, how they explore the ontologies, and how they reuse classes from different ontologies. Additionally, through three real-world scenarios, we not only analyze the usage of ontologies for annotation tasks but also compare it to the browsing and querying behaviors of BioPortal users. For our investigation, we use several different visualization techniques. To inspect large amounts of interaction, reuse, and real-world usage data at a glance, we make use of and extend PolygOnto, a visualization method that has been successfully used to analyze reuse of ontologies in previous work. Our results show that exploration, query, reuse, and actual usage behaviors rarely align, suggesting that different users tend to explore, query and use different parts of an ontology. Finally, we highlight and discuss differences and commonalities among users of BioPortal.

Keywords: data visualization, ontology reuse, ontology exploration, user behavior, knowledge exploration, log analysis

Suggested Citation

Kamdar, Maulik and Walk, Simon and Tudorache, Tania and Musen, Mark, Analyzing User Interactions with Biomedical Ontologies: A Visual Perspective (2018). Journal of Web Semantics First Look 49_0_2. Available at SSRN: https://ssrn.com/abstract=3199318 or http://dx.doi.org/10.2139/ssrn.3199318

Maulik Kamdar (Contact Author)

Stanford University - Center for Biomedical Informatics Research ( email )

1265 Welch Road
Stanford, CA
United States

Simon Walk

Stanford University - Center for Biomedical Informatics Research ( email )

1265 Welch Road
Stanford, CA
United States

Tania Tudorache

Stanford University - Center for Biomedical Informatics Research

1265 Welch Road
Stanford, CA
United States

Mark Musen

Stanford University - Center for Biomedical Informatics Research

1265 Welch Road
Stanford, CA
United States

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