1. A method for transforming narrative content into structured 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 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; and identifying one or more clinical assertion elements which define a clinical assertion and assigning a clinical assertion element label to at least one clinical assertion element of the one or more clinical assertion elements based on a clinical model, wherein the label assigned to the at least one clinical assertion element is selected from a predetermined list, wherein the list is predetermined based on a clinical assertion type.