Indiana University-Purdue University Indianapolis (IUPUI) / Drug-Drug Interaction (DDI) is one of the major causes of adverse drug reaction (ADR) and has been demonstrated to threat public health. It causes an estimated 195,000 hospitalizations and 74,000 emergency room visits each year in the USA alone. Current DDI research aims to investigate different scopes of drug interactions: molecular level of pharmacogenetics interaction (PG), pharmacokinetics interaction (PK), and clinical pharmacodynamics consequences (PD). All three types of experiments are important, but they are playing different roles for DDI research. As diverse disciplines and varied studies are involved, interaction evidence is often not available cross all three types of evidence, which create knowledge gaps and these gaps hinder both DDI and pharmacogenetics research. In this dissertation, we proposed to distinguish the three types of DDI evidence (in vitro PK, in vivo PK, and clinical PD studies) and identify all knowledge gaps in experimental evidence for them. This is a collective intelligence effort, whereby a text mining tool will be developed for the large-scale mining and analysis of drug-interaction information such that it can be applied to retrieve, categorize, and extract the information of DDI from published literature available on PubMed. To this end, three tasks will be done in this research work: First, the needed lexica, ontology, and corpora for distinguishing three different types of studies were prepared. Despite the lexica prepared in this work, a comprehensive dictionary for drug metabolites or reaction, which is critical to in vitro PK study, is still lacking in pubic databases. Thus, second, a name entity recognition tool will be proposed to identify drug metabolites and reaction in free text. Third, text mining tools for retrieving DDI articles and extracting DDI evidence are developed. In this work, the knowledge gaps cross all three types of DDI evidence can be identified and the gaps between knowledge of molecular mechanisms underlying DDI and their clinical consequences can be closed with the result of DDI prediction using the retrieved drug gene interaction information such that we can exemplify how the tools and methods can advance DDI pharmacogenetics research. / 2 years