1. A method for transforming narrative content into structu ed output that defines where individual information resides within the output, the method comprising the steps of: receiving narrative content; scanning the narrative content using a natural language processing (NLP) engine to identify at least one section and at least one clinical assertion within that section; extracting information from the narrative content, wherein the extracted information includes clinical assertions and contextual information; identifying one or more elements which define a clinical assertion and assigning a label to at least one element based on a clinical model.