Analyzing User Interactions with Biomedical Ontologies: A Visual Perspective

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.

BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

“…All access to BioPortal, either via the WebUI or through the API, is captured in the BioPortal Apache access logs, which record the request URL, the time of request, and the IP address of the requestor. We have previously used the information stored in these access logs to identify categories of users accessing ontologies in BioPortal [6], to study ontology reuse [4], and to visualize ontology exploration and query patterns [5]. …”

“…VisIOn can visualize a dataset in 4 different perspectives: i) scatter plot, ii) volcano plot, iii) word cloud, and iv) PolygOnto visualizations [5]. The scatter plot perspective allows the user to select the features to display on the X- and Y-axes, and then visualizes the aggregate statistics along with the structural features of the classes (Figure 2).…”

“…The height of the polygon represents the number of hierarchical layers in the ontology, whereas the width represents the number of classes in each layer. We developed the method to generate the PolygOnto visualization for an ontology and its sequence datasets in our prior work [5]. …”

“…For this reason, we developed the PolygOnto visualization [5] (Figure 3) that exploits the class hierarchy to reveal regions in an ontology where users tend to explore and query more. Classes are arranged in different layers based on the maximum depth from the root class in the ontology.…”