Checking class labels against naming conventions: First experience with the OntoCheck Protégé plugin

Daniel Schober, Vojtěch Svátek, Martin Boeker

Research output: Contribution to journalConference articlepeer-review

Abstract

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 engi-neering efforts and test a variety of different ontologies on preva-lence 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 re-quirements drawn from naming conventions themselves, mismatch-es 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 mis-matches 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 appli-cation of OntoCheck supports the verification of naming conventions and will ultimately ease string based ontology alignment.

Original languageEnglish
JournalCEUR Workshop Proceedings
Volume897
StatePublished - 2012
Externally publishedYes
Event3rd International Conference on Biomedical Ontology 2012, ICBO 2012 - Graz, Austria
Duration: 21 Jul 201225 Jul 2012

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