1. A method for use with a Clinical Documentation Improvement (CDI) system implemented via at least one first processor and processing medical documentation input at least in part by a clinician, the CDI system configured to communicate with a medical documentation system that also processes the medical documentation and is implemented via at least one second processor, 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, and 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, the method comprising: with the CDI system implemented via the at least one processor, receiving from the medical documentation system a structured data set including at least some information relating to one or more medical facts and including information indicating that the medical documentation system automatically extracted the one or more medical facts from text documenting a patient encounter, wherein the information related to the one or more medical facts comprises a first medical fact and a first confidence score produced by the medical documentation system indicating a confidence of the medical documentation system that the first medical fact was accurately extracted from the text documenting the patient encounter, the information relating to one or more medical facts further comprising at least one clarification request generated by the medical documentation system, the at least one clarification request requesting clarification regarding at least the first medical fact of the one or more medical facts and/or regarding at least a portion of the text documenting the patient encounter; in response to determining that the first confidence score is below a first threshold, prompting a user of the CDI system regarding the at least one clarification request; receiving from the user of the CDI system, in response to the prompt regarding the at least one clarification request, at least one input providing clarification regarding the first medical fact and/or the at least the portion of the text documenting the patient encounter; and in response to receiving the at least one input, transmitting a clarification response to the medical documentation system addressing the at least one clarification request, the clarification response comprising an indication of whether to prompt the clinician regarding the at least one clarification request.