Modest use of ontology design patterns in a repository of biomedical ontologies

Ontology Design Patterns (ODPs) provide a means to capture best practice, to prevent modeling errors, and to encode formally common modeling situations for use during ontology development. Despite the popularity of ODPs and supposed positive effects from their use, there is scant empirical evidence of their level of adoption in real world ontologies or on their effectiveness. Knowing the goals of ODPs, they may assist in the development of large-scale biomedical ontologies. Before studying ODP effectiveness and applicability, we ask the following questions to understand better the landscape of ODP use: Are ODPs used in biomedical ontologies? Which patterns do the ontology developers use? In which ontologies? How frequently are patterns used? To answer these questions, we determined the adoption of ODPs from two popular ODP libraries among the ontologies in BioPortal, a large ontology repository that contains over 300 biomedical ontologies. We encoded 68 ODPs from two online libraries in the Ontology Pre-Processor Language, and, using these encodings, determined ODP prevalence in BioPortal ontologies. We found modest use of ODPs, with 33% of the ontologies containing at least one pattern. Upper Level Ontology, Closure, and Value Partition were the three most commonly used patterns, occurring in 20%, 9%, and 6% of the BioPortal ontologies, respectively. The low prevalence of ODPs may be due to lack of proper tooling, lack of user knowledge of and education about them, the age of the ontologies in the repository, or the specificity of some ODPs. We noted that there is a tension between the high expressivity of many ODPs and the goal of maintaining low expressivity of some biomedical ontologies. Additional tooling is necessary to make ODPs more accessible to domain experts. Furthermore, we suggest that ODPs may be developed in a bottom-up fashion, much like software-design patterns.