Checking Class Labels against Naming Conventions: First experiences with the OntoCheck Protégé plugin

Background: Although ontology naming conventions have been proposed by policy makers, the lack of tool support for testing and enforcing naming practices has hindered widespread compliance. We have developed OntoCheck, a Protégé plugin, which allows testing labels in an ontology on naming inconsistencies. Objective: We report on initial experience in applying the tool in different settings and show that OntoCheck contributes to quality assurance in a test-set of ontologies. Methods: We apply OntoCheck in four different ontology engineering efforts and test a variety of different ontologies on prevalence of naming issues. For each, we analyze the percentages of class names and labels violating outlined conventions and correlate the check types to the set of OBO Foundry naming conventions. Results: Application of OntoCheck revealed that heterogeneity in class labels is still a common feature, even in release versions of ontologies, and that many of these could be detected and rectified by tool support. Nearly half of the OBO Foundry naming conventions could be assisted by OntoCheck, the remaining fraction relying on more complicated parsing and availability of lexica. Besides requirements drawn from naming conventions themselves, mismatches in string-based ontology alignment algorithms are identified as sanity check on the impact of labelling consistency. Analysing the prevalence of false positive and negative ontology alignment mismatches could prove valuable in deriving new naming conventions and test their effects in cross ontology harmonization efforts. Conclusion: Our results show that typographical and syntactical labelling heterogeneity can be improved by tool support. The application of OntoCheck supports the verification of naming conventions and will ultimately ease string based ontology alignment.