A method and system for generating nested mapping specifications and transformation queries based thereon. Basic mappings are generated based on source and target schemas and correspondences between elements of the schemas. A directed acyclic graph (DAG) is constructed whose edges represent ways in which each basic mapping is nestable under any of the other basic mappings. Any transitively implied edges are removed from the DAG. Root mappings of the DAG are identified. Trees of mappings are automatically extracted from the DAG, where each tree of mappings is rooted at a root mapping and expresses a nested mapping specification. A transformation query is generated from the nested mapping specification by generating a first query for transforming source data into flat views of the target and a second query for nesting flat view data according to the target format. Generating the first query includes applying default Skolemization to the specification.