In the MaSyMoS (Management System for Models and Simulations) project, a graph-based data storage for efficient search and similarity determination in simulation studies of systems biology and systems medicine is designed based on a graph database. For this purpose, information from different domains, e.g. models, simulation descriptions and ontologies, is extracted and linked in a suitable way. This allows querying knowledge as a classical word-based search and combines it with structured queries on knowledge graphs.