To reach the stated goal of the flexibility of data structures and support users creating semantic annotated scientific texts, the WissKI project developed an interface to integrate semantic back-ends like a triple store. Triple stores generally provide several interfaces for communication. The most common language for interaction with a triple store is SPARQL, which is a recommendation of the World Wide Web Consortium (W3C) since the end of 2008 and therefore is used in the WissKI software. The triple store builds the foundation of a middle-ware that is able to deal with the semantic base technology like ontologies consisting of concepts and properties and instances of them. Such ontologies can be defined in different common languages to serialize them in a machine-readable way. Ontologies in computer science are normally based on formal logics with well founded semantics.These are used to define, categorize, describe and infer knowledge in a formal way. We decided to use the Web Ontology Language (OWL), which is developed by the W3C. OWL1 became a recommendation in 2004, and a revised and extended OWL2 became a recommendation in 2009. OWL consists of three levels of expressiveness. OWL DL is the optimal language for this task in the WissKI project as it is a machine-processable and therefore "understandable" formalism with a maximum of expressiveness while retaining computability. The DL in OWL DL stands for Description Logics and OWL DL 1.0 is a syntactic equivalent to the DL SHOIN(D). Ontologies in OWL DL have a lot of advantages: The syntax is readable by computers and humans, the formally defined semantics give expressions a clear meaning and SHOIN(D) allows decidable inferences, but high expressivity, the computation of semantics supports modelling and therefore the creation of ontologies. There are already implemented tools like editors (e.g. Protégé), reasoners (e.g. Racer, Hermit, Pellet, Fact++) and other semantic web software. In contrast to other logic based systems, OWL follows the idea of open world semantics, which, for example, do not interpret unknown facts as false ones. Most of the web software with support for OWL DL uses the serialisation in RDF/XML syntax.