Hyper-graphs offer the opportunity to formulate logical statements about their components, for example, using Horn clauses. Several models of Information Systems can be represented using hyper-graphs as the workflows, i.e., the business processes. During the modeling of Information Systems, many constraints should be maintained during the development process. The models of Information Systems are complex objects, for this reason, the analysis of algorithms and graph structures that can support the consistency and integrity of models is an essential issue. A set of interdependencies between models and components of architecture can be formulated by functional dependencies and can be investigated via algorithmic methods. Information Systems can be perceived as overarching documents that includes data collections; documents to be processed; and representations of business processes, activities, and services. Whe selecting and working out an appropriate method encoding of artifacts in Information Systems, the complex structure can be represented using hyper-graphs. This representation enables the application of various model-checking, verification, and validation tools that are based on formal approaches. This paper describes the proposed representations in different situations using hyper-graphs, moreover, the formal, algorithmic-based model-checking methods that are coupled with the representations. The model-checking methods are realized by algorithms that are grounded in graph-theoretical approaches and tailored to the specificity of hyper-graphs. Finally, the possible applications in a real-life enterprise environment are outlined.