This document discusses large-scale integration of biological data and text through several databases and resources created by the author's lab, including STRING and STITCH, which integrate protein-protein interaction data from multiple sources. It describes using text mining to extract protein interactions from literature through named entity recognition, relationship extraction, and integration of the results with interaction data from experimental and computational sources. Clinical applications including using Danish health registries and text mining of medical records to discover new drug-drug interactions and adverse drug reactions are also summarized.