A method and system for specifying, in a schema mapping framework, a mapping between a source schema and a target schema. The source and target schemas are schemas included in respective groups of registered, heterogeneous schemas. The source and target schemas may be of different types. Serialized versions of the source and target schemas include source objects and target objects, respectively. A mapping model is serialized into mapping objects that include logical references representing the source objects and logical references representing the target objects. The logical references are resolved to the source objects and target objects, thereby storing pointers to the source objects and to the target objects. After resolving the logical references, the mapping model includes the logical references and the pointers to the source and target objects.