The completion of a high quality comprehensive sequence of the human genome has lead to the discovery of genetic links to complex diseases and the development of target drugs. Population genetic databases (PGDs) are a powerful resource to the systematic study of the genetic component of disease; in the quest to understand the impact of genetic factors on drug response data from laboratory experiments, computational methods and clinical studies must be integrated. The establishment of a pharmacogenomics knowledge base entails complex information management balanced with the appropriate legal and ethical standards. This article reviews some of the ontology development challenges and examines the need to establish a legal structure which creates the proper intellectual property incentives to develop PGDs and the ethical standards that must be upheld so that the terms of informed consent are legitimate.