A computer system for integrating medical information using the Unified Medical Language System (UMLS) as a taxonomy of medical terms includes a learner module for learning from training data concept classifiers for a source ontology and a target ontology, a mapper module for generating associations between source and target ontology classifiers using the UMLS, an annotator module for extracting knowledge from test data using source and target ontology classifiers and UMLS, and a feedback module for ranking associations according to a level or certainty, and presenting those associations that fall below a predefined level of certainty to a user for correction.