Design and Development of an Integrated Formal Ontology for Fungal Genomics

With the substantial increase in stored scientific data of various types a major challenge of the post-genomic era is to access the knowledge stored in a myriad of complex databases and other resources across the web. Ontologies can play an important role in bioinformatics, as they do in other disciplines, where they will provide a shared source of precisely defined terms that can be communicated across people and applications. The Ontology Web Language (OWL) is an ontology language that has an easy to use frame feel, yet at the same time allows users to exploit the full power of an expressive Description Logic (DL). The thesis presents a formal integrated bio-ontology design and implementation case study in the area of fungal genomics to provide simplified access to units of intersecting information from different biological databases and existing bio-ontologies. We demonstrate the capacity of the ontological conceptualization through a series of industry related queries. Using OWL-DL highlights the features of the combination of a frame representation of OWL framework and expressive Description Logics. We also used Racer as DL reasoner to build and maintain sharable ontologies by revealing inconsistencies, hidden dependencies, redundancies and misclassifications