@conference {ICBO_2018_23, title = {ICBO_2018_23: Prot{\'e}g{\'e} 5.5 {\textendash} Improvements for Editing Biomedical Ontologies}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {

We present Prot{\'e}g{\'e} 5.5, a significant update to the Prot{\'e}g{\'e} Desktop software, which contains new features that are geared towards editing biomedical ontologies. This version of Prot{\'e}g{\'e} contains user-interface enhancements and optimizations that should make the browsing and editing of OBO-library-style biomedical ontologies easier, faster and more efficient when compared to previous versions of Prot{\'e}g{\'e}.

}, keywords = {Biomedical Ontology Editing, OWL, Prot{\'e}g{\'e}}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_23.pdf }, author = {Matthew Horridge and Rafael S Gon{\c c}alves and Csongor I Nyulas and Tania Tudorache and Mark Musen} } @conference {ICBO_2018_31, title = {ICBO_2018_31: Test-driven Ontology Development in Prot{\'e}g{\'e}}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {

Over the past decade, various quality assurance methodologies have emerged in the field of software engineering for preventing, detecting, and fixing faults and bugs in software. In particular, Test-driven Development (TDD) is now a popular quality assurance technique whereby extensive usage of test cases can be used to enforce the correctness of software artifacts. While testing has made its way into the field of ontology engineering, where some techniques for testing ontologies are now used in prominent biomedical ontology projects, Test-driven Development has yet to achieve significant uptake. In this paper we propose a Logic-Based Test-driven Ontology Development methodology, which takes cues from Test-Driven Development in the field of software engineering. Our hope is that this will encourage a "test-first" approach to ontology engineering and that it will form part of the arsenal available to ontology engineers in order to help them produce and maintain high quality ontologies. Test cases in our framework are represented by simple statements describing expected and/or unwanted logical consequences of an intended ontology. As with Test-driven Development in software engineering, our approach encourages small, frequent iterations in the testing and development life-cycle. We provide and present tool support for our approach in the form of OntoDebug {\textendash}- a plug-in for the ontology editor Prot{\'e}g{\'e}.

}, keywords = {ontology quality assurance, Prot{\'e}g{\'e} Plug-In, Test-Driven Ontology Development}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_31.pdf }, author = {Konstantin Schekotihin and Patrick Rodler and Wolfgang Schmid and Matthew Horridge and Tania Tudorache} } @conference {ICBO_2018_9, title = {ICBO_2018_9: A Prot{\'e}g{\'e} Plug-In for Test-Driven Ontology Development}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {

Ontology development is a hard and often error-prone process, which requires ontology authors to correctly express their domain knowledge in a formal language. One way to ensure the quality of the resulting ontology is to use test cases, similarly to the best practices in software development. For ontology development, test cases can be specified as statements describing expected and/or unwanted logical consequences of an ontology. However, verifying the test cases and identifying the ontology parts that cause their violation is a complex task, which requires appropriate tool support. In this demo, we present OntoDebug {\textendash} a plug-in for the Prot{\'e}g{\'e} editor {\textendash} that supports test-driven ontology development. OntoDebug can automatically verify whether the ontology satisfies all defined test cases. If any test case is violated, the plug-in assists the user in debugging and repairing the ontology in an interactive way. The plug-in asks a series of questions about the ontology to pinpoint the faulty axioms. Once a fault is repaired, all answers that the author provided in the interactive debugging session may be converted into test cases, thus preserving the additional knowledge, which can be used in future testing of the ontology.

}, keywords = {Fault Detection in Ontologies, Fault Localization in Ontologies, Fault Repair in Ontologies, Ontology Debugging, Prot{\'e}g{\'e} Plug-In, Test-Driven Ontology Development, User Interaction}, url = {http://ceur-ws.org/Vol-2285/ICBO_2018_paper_9.pdf }, author = {Konstantin Schekotihin and Patrick Rodler and Wolfgang Schmid and Matthew Horridge and Tania Tudorache} }