Phenotyping methods aiming to produce high-fidelity time-dependent phenotypes in a specific context with personalized interpretation are challenging, especially given the complexity of physiological systems and data quality. We present a three-stage methodological phenotyping pipeline based on a mechanistic physiological model framework applied to the glucose-insulin system of ICU patients from electronic health record data. Balancing flexibility and biological fidelity, the pipeline within the data assimilation (DA) framework is used to compute physiologically-anchored phenotypes that are high-fidelity, personalized, time-sensitive, and interpretable using data present in real-time ICU settings. We construct the computational phenotyping pipeline such that it is generalizable and we demonstrate the pipeline's accuracy and reliability through external data evaluation using electronic health record data and clinical face validation.