In our days there is no single test or biomarker that can predict whether a particular person will develop Parkinson Disease and a definitive diagnosis is only possible after death, with postmortem analysis. Recent discoveries have highlighted that defects in mitochondrial dynamics are associated with neurodegenerative disease. In this paper the general architecture of an integrated multi-scale ontology-based modeling technology for early diagnosis of PD and for progress monitoring is proposed. The proposed model will be used to identify physics and biology-based biomarkers of processes occurring at radically different scales, from cell to whole body.