The City Anatomy, an analogy to the human anatomy and its dynamic physiology, is an organizing framework for the City Protocol. It creates a foundation upon which to build a collaborative platform and tools to support effective city governance, evaluation and transformation. It offers a common language describing the city ecosystem as three key system elements: a set of physical structures (Structure); the living entities that make up a city’s society (Society); and the flow of interactions between them (Interactions). In so doing, City Anatomy helps understanding and mapping interconnections between these city systems.