External Sources:

External ontologies:
Chemical Ontology: Chemical entities of biological interest
Gene Ontology: GO
Protein Ontology: PO
Pathway Ontology: Biopax
Disease Ontology: DO
chemical information: cheminfo
Systems Biology Ontology:SBO
Pharmagenomics: from Michel Dumontier’ lab
BioAssay Ontology: http://www.bioassayontology.org/
Translational Medicine Ontology http://esw.w3.org/HCLSIG/PharmaOntology
Other ontologies could be found at: http://www.obofoundry.org/

External Vocabularies:
MeSH, NCI Thesaurus, ATC System, Adverse Event (CTCAE)

External Data Schema:
http://chem2bio2rdf.wikispaces.com/Datasets
Other sources:
http://bioportal.bioontology.org

Related works:

Choi: A Semantic Web Ontology for Small Molecules and Their Biological Targets
Qu: Inferring novel disease indications for known drugs by semantically
linking drug action and disease mechanism relationships
Dumontier: Towards pharmacogenomics knowledge discovery with the semantic web