Our long-term objective is to develop a software toolbox for pre-embodiment design of complex and heterogeneous systems, such as cyber-physical systems. The novelty of this toolbox is that it uses system manifestation features (SMFs) for transdisciplinary modeling of these systems. The main challenges of implementation of the toolbox are functional design- and language-independent computational realization of the warehouses, and systematic development and management of the various evolving implements of SMFs (genotypes, phenotypes, and instances). Therefore, an information schema construct (ISC) based approach is proposed to create the schemata of the associated warehouse databases and the above-mentioned SMF implements. ISCs logically arrange the data contents of SMFs in a set of relational tables of varying semantics. In this article we present the ISCs necessary for creation of genotypes and phenotypes. They increase the efficiency of the database development process and make the data relationships transparent. Our follow-up research focuses on the elaboration of the SMF instances based system modeling methodology.