The FungalWeb Ontology: Semantic Web Challenges in Bioinformatics and Genomics

Bioinformatics and genomics cover a wide range of different data formats (i.e. annotations, pathways, structures, sequences) derived from experimental and in-silico biological analysis which are stored, used, and manipulated by scientists and machines. The volume of this data is huge and usually distributed in different locations, and often frequently being updated. FungalWeb is the first project of its kind in Canada to focus on bringing semantic web technology to genomics. It aimed to bring together available expertise in ontologies, multi-agent systems, machine learning and natural language processing to build a tailored knowledgebase and semantic systems of direct use to the scientific discovery process in the domain of fungal genomics [1]. We describe the FungalWeb Ontology which is a large-scale integrated bio-ontology in the domain of fungal genomics using state-of-the-art semantic technologies. The ontology provides simplified access to units of intersecting information from different biological databases and existing bio-ontologies. In particular, the FungalWeb ontology is being used as a core for a semantic web system. This system can be used by human, bioinformatics applications or some intelligent systems for ontology-based information retrieval to provide extended interpretations and annotations. [2]