Discerning the genetic contributions to complex human diseases is a challenging mandate that demands new types of data and calls for new avenues for advancing the state-of-the-art in computational approaches to uncovering disease etiology. Systems approaches to studying observable phenotypic relationships among diseases are emerging as an active area of research for both novel disease gene discovery and drug repositioning. Currently, systematic study of disease relationships on a phenome-wide scale is limited due to the lack of large-scale machine understandable disease phenotype relationship knowledge bases. Our study innovates a semi-supervised iterative pattern learning approach that is used to build an precise, large-scale disease-disease risk relationship (D1 xe2x86x92 D2) knowledge base (dRiskKB) from a vast corpus of free-text published biomedical literature.