Below is the reference and link to the paper (presented at Bio-Ontologies, ISMB 2008) I mentioned during last week's HCLS call... Angela X. Qu et al. "Tamoxifen to Systemic Lupus Erythematosus:Constructing a Semantic Infrastructure to Enable Mechanism-based Reasoning andInference from Drugs to Diseases"
The paper can be found along with others in http://www.bio-ontologies.org.uk/download/Bio-Ontologies2008.pdf What I think is worth noting in this paper, is that in addition to SPARQL-endpoints and ontologies, there are additional ways of finding patterns and mining information from RDF structures based on graph-theoretic methods. Eric