Ontological analysis of controlled vocabularies used in PSI/MSI supported XML standards (original) (raw)
Besides a ple thora of formal ontologies, the requirement for simple data annotation has led to an increased use o f so called controlled vocabularies (CV) in multiple omics communities . We analyze two of those CVs from an ontological viewpoint, highlight typical modelling errors and propose more adeq uat solutions. Discovered errors are discussed in the light of the OOPS ontology pitfa ll framework and the OBO Foundry naming conventions. As a result the CVs could be improved and the OOPS catalogue could be amended and ex pand d with new, previously missing error categories . In an outlook we discuss potential reasons for the error prevalence and analyse what criticism is justified for CV semantics d what ‘errors’ are more valid for formal ontologies rather than CVs. We conclude that although many design principles valid for description logics ontol gies are not relevant for semantically flat CVs and in tur n there is a need for CV-best-practice s that are not appropriate for descr...
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