The development of standards for biological pathways has led to a huge amount of model data stored in a variety of different formats represented in XML (e. g. SBML) or OWL (e. g. BioPAX). Thus, there is an urgent need for the conversion of data between different formats. Especially the comparison of XML and OWL data is hard to realize, a fact that hampers the integration of data in the area. Addressing this problem, the following article proposes a general, semi-automatic solution of such a conversion. We propose a transformation of XML Schema based data into an OWL format. The general solution presented here, will support biologists by offering them a way to query data of any format and as well compare different data files or schemas to each other using OWL as a common format for matching and providing a backwards transformation to XML Schema. The paper presents a first architectural approach and evaluates it using a test setup of the suggested architecture. The evaluation showed that the approach is promising.