Domain model and domain modeling is an important part of software engineering and domain analysis in general. There are many domain modeling approaches available and being used today, however these tend to be based on "best practices" and not based on a formal domain model. This is an essential problem, but in particular for software engineering this leads to a lack of formal connection between the domain model and the solution model. In order this leads to a gap between the domain and the solution, thus resulting in failed software development projects, overrun budgets and/or bad quality software. By avoiding a proper domain analysis at the beginning of software engineering with a formal domain model it is not possible to perform scope and content validation of the domain model, it is not possible to do a formal transformation from domain model to the solution model, and thus it is not possible to formally trace the elements of the domain model to the solution model. The main goal of this doctoral thesis titled “The Integrated Domain Modeling: An Approach & Toolset for Acquiring a Topological Functioning Model” is to improve the process of domain analysis and sequentially lowering cost of software development projects, raising the quality of produced software and enabling their success by improving the understanding of the domain at the beginning of software engineering process. To achieve this goal a novel domain modeling approach and a supporting toolset has been developed by the author for acquiring a mathematically formal domain model that is transformable and can be used as the Computation Independent Model (CIM) within Model Driven Architecture (MDA). This approach is called “Integrated Domain Modeling” (IDM) and is based on the Topological Functioning Model (TFM), Ontology and Use Cases. This approach provides a way to use directly use Ontology as input for software engineering by exploiting Use Cases and Natural Language Processing. The supporting toolset is based on MDA standards and provides a model-to-model transformation for acquiring an initial TFM automatically from formally defined domain knowledge (declarative and procedural knowledge). The doctoral thesis consists of 224 pages, 52 figures, 4 tables, and 10 appendices. Bibliography includes 100 literary sources.