1. Use cases proposed in Chem2Bio2RDF
The desirable ontology should be able to answer the questions proposed in Chem2Bio2RDF, where we use SPARQL to deal with them. However, without ontology, writing of sparql is tedious and requires the understanding of RDF schema.

2. Interesting cases from translational medicine ontology project

3. Cases in the paper A Semantic Web Ontology for Small Molecules and Their Biological Targets:

4. Cases in the paper: Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships