1. A method for use with a medical documentation system implemented via at least one processor and processing medical documentation input at least in part by a clinician, the medical documentation system configured to communicate with a Clinical Documentation Improvement (CDI) system that also processes the medical documentation, wherein the medical documentation system implemented via the at least one processor analyzes text included in the medical documentation to extract medical facts expressed in the medical documentation and identify opportunities for clarification of the medical documentation, and wherein the CDI system includes a user interface by which to present the medical documentation to a CDI specialist and receive from the CDI specialist new information to include in the medical documentation to clarify the medical documentation and to receive from the CDI specialist identification of opportunities for clarification of the medical documentation, the CDI specialist being a human user of the CDI system, the method comprising: with the medical documentation system implemented via the at least one processor, for each fact of at least one medical fact extracted by the medical documentation system from text of the medical documentation documenting a patient encounter between a patient and the clinician, evaluating a confidence score for the fact indicating a confidence of themedical documentation system that the fact was correctly extracted from the medical documentation system; and selecting, with the medical documentation system and based at least in part on a result of the evaluating, whether to transmit the fact to the CDI system for review by the CDI specialist or to communicate the fact to a clinician for review; and in response to selecting to transmit one or more medical facts to the CDI system, transmitting to the CDI system a structured data set including at least some information relating to the one or more medical facts and including information indicating that the medical documentation system automatically extracted the one or more medical facts from the text documenting the patient encounter.