Methods and systems for patient participatory care and monitoring are provided for applications including respiratory care, ECG monitoring, capnography, infusion pump alarm prevention/management, pressure sore prevention, incentive spirometry, consciousness monitoring during sedation, pain management and other care and monitoring modalities. A patient in-the-loop system includes an input interface for receiving data acquired from a monitoring, controlling or sensing device, a storage device for storing the data at a first location, and a processor for analyzing artifacts in the data and determining whether the patient provided a deliberate action with respect to the device as a response to a prompt or query. The processor can further initiate a variety of prompts and/or output queries stored in the storage device at a second location to the patient. The data derived from these patient-in-the-loop techniques are formatted to be received and interpreted by electronic medical record and electronic record keeping systems.