Hunter and Bassingthwaithe define the Physiome as a set of multiscale, interacting mathematical models of physiology. Although available model repositories are an initial step toward this vision, it is a critical next step to develop computer-readable annotation for connecting codewords across models. Current hand-crafted model-building methods must be formalized and standardized to better support knowledge interaction and sharing. In particular, we argue for semantic annotations as a way of communicating the biophysical meaning of individual model codewords. Once annotated in a computable format, we can automatically find and connect models based on the annotation semantics of the biological entities and physiological properties. In this talk, we present our approach to semantic annotation, using standard bio-ontology terms to relate physiological properties (e.g. pressure), to anatomical entities (e.g. blood). In turn, we use these annotations to semi-automatically find relevant models from repositories, and ultimately merge those models where appropriate. We present our results with SemGen, a prototype tool, for both building annotations and merging models, even across different modeling languages. If successful, our approach to develop interacting model repositories could accelerate model sharing and integration, and research that depends on the construction of complex models.