The NCBO Annotator Workflow extracts terms from the clinical notes of patients: (1) We obtain a lexicon of over 2.8-million terms from the NCBO BioPortal library. (2) We use the NCBO Annotator to rapidly find those terms in clinical notes—which we call annotations. (3) We apply NegEx trigger rules to separate negated terms. (4) We compile terms (both positive and negative) into a temporally ordered series of sets for each patient and combine them with coded and structured data when possible. (5) We reason over the structure of the ontologies to normalize and to aggregate terms for further analysis.