owl:sameAs Considered Harmful to Provenance
GOTO was once a standard operation in most computer programming languages. Edsger Dijkstra argued in 1968 that GOTO is a low level operation that is not appropriate for higher-level programming languages, and advocated structured programming in its place. Arguably, owl:sameAs in its current usage may be poised to go through a similar discussion and transformation period. In biomedical research, the provenance of information gathered is nearly as important as, and sometimes even more important than, the information itself. owl:sameAs allows someone to state that two separate descriptions really refer to the same entity. Currently that means that operational systems merge the descriptions and at the same time, merge the provenance information, thus losing the ability to retrieve where each individual description came from. This merging of provenance can be problematic or even catastrophic in biomedical applications that demand access to provenance information. Based on our knowledge of integration issues of data in biomedicine, we give examples as use cases of this issue in biospecimen management and experimental metadata representations. We suggest that systems using any construct like owl:sameAs must provide an option preserve the provenance of the entities and ground assertions related to those entities in question.