Methods for developing an ontology of pharmacogenomics (PGx) relationships starting from a lexicon of key pharmacogenomic entities and a syntactic parse is described. The syntactic structure of PGx statements is used to systematically extract commonly occurring relationships and to map them to a common schema. In an embodiment, extracted relationships have a 70-87.7% precision and involve not only key PGx entities such as genes, drugs, and phenotypes (e.g., VKORC1, warfarin, clotting disorder), but also critical entities that are frequently modified by these key entities (e.g., VKORC1 polymorphism, warfarin response, clotting disorder treatment).