One of the major weaknesses of current research on the Semantic Web (SW) is the lack of proper means to represent and reason with uncertainty. A number of recent efforts from the SW community, the W3C, and others have recently emerged to address this gap. Such efforts have the positive side effect of bringing together two fields of research that have been apart for historical reasons, the artificial intelligence and the SW communities. One example of the potential research gains of this convergence is the current development of Probabilistic OWL (PR-OWL), an extension of the OWL Web Ontology Language that provides a framework to build probabilistic ontologies, thus enabling proper representation and reasoning with uncertainty within the SW context. PR-OWL is based on Multi-Entity Bayesian Networks (MEBN), a first-order probabilistic logic that combines the representational power of first-order logic (FOL) and Bayesian Networks (BN). However, PR-OWL and MEBN are still in development, lacking a software tool that implements their underlying concepts. The development of UnBBayes-MEBN, an open source, Java-based application that is currently in alpha phase (public release March 08), addresses this gap by providing both a GUI for building probabilistic ontologies and a reasoner based on the PR-OWL/MEBN framework. This work focuses on the major challenges of UnBBayes-MEBN implementation, describes the features already implemented, and provides an overview of the major algorithms, mainly the one used for building a Situation Specific Bayesian Network (SSBN) from a MEBN Theory.