The paper presents the issue of mapping database schema within the context of possible partial loss of their semantics. Moreover, authors present methodology of mapping relational models to association-oriented model and briefly present the association-oriented metamodel itself, which is one of the co-authors proposition for novel database metamodel. It is the proposition of productive tool, which is free of other metamodels' defects. The issues described within the paper have been presented in terms of the case study, which is the typical example of modeling problems that are concerned within interest of bioinformatics.