Sebastian, Benjamin, Elvira, Andra, Andrew, Kudos on your progress with an OWL-centric approach to knowledge representation. The community has been incorporating OWL concepts into property definitions and ontology development on-wiki for some time, but yours is the first Wikidata group I'm aware of that has incorporated Protege into the process.
We think that using ontologies brings several advantages The examples you cite seem like good ideas and I support them. I would also suggest considering how the Wikidata ontologies we develop fit into established ontologies in the Semantic Web. For example, the OBO Foundry (http://www.obofoundry.org/) is by far the world's most widely used group of biomedical ontologies [1, 2]. Those ontologies are rooted in the Basic Formal Ontology (BFO). OWL helps a great deal in being interoperable with those works, but a further ontological commitment tends to be needed for easy compatibility. Is your gene-disease interaction ontology compatible with BFO, and the OBO ontologies rooted in it? Cheers, Eric https://www.wikidata.org/wiki/User:Emw 1. http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html 2. https://scholar.google.com/scholar?cites=13806088078865650870
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