An example that comes up all the time in life sciences is the non-static naming of proteins and genes. If you look across databases (and sometimes even within the same database), the same gene or protein is named differently. This naming problem extends to the URIs in RDF versions of these databases.

Merging these datasets with a conventional RDBMS requires identifiying a common key that links identical proteins/genes or otherwise provide a translation table that holds all of the identifiers and their database sources to link common entities.

RDF presents a unique opportunity to "automatically" aggregate the properties for nodes that represent the same protein or gene. In thinking through this, a translation "table" of triples would still be required, but linking all of the data sources could be done with a simple rule.

For instance, if we used the BioPAX ontology, an OWL rule (I know Oracle doesn't yet support OWL, but this is a good reason to) could state that any physicalEntity (e.g. protein, gene, etc.) that matched another protein or gene entity via a cross-referenced identifier should be linked with an owl:sameAs property. Right now this is possible (albeit slowly) using open-source tools such as Jena and Pellet.

The real magic would be that if some API function could present this pair of identical nodes as a single node to the user or programmatically to the developer.


Does this make sense? I'd love to speak with you more about this.