Database transformations are a frequent problem for data managers supporting scientific databases, particularly those connected with the Human Genome Project. The databases involved frequently contain complex data-structures not typically found in conventional databases, such as arbitrarily nested records, sets, variants and optional fields, as well as object identities and recursive data-structures. Furthermore, programs implementing the transformations must be frequently modified since the databases involved evolve rapidly, as often as 3 to 4 times a year. We present in this paper a language (WOL) for specifying transformations between such databases and describe its implementation in a system called Morphase. Optimizations are performed at all stages, with significant impact on the compilation and execution time of sample transformations.