Semantic web infrastructure for fungal enzyme biotechnologists

The FungalWeb Ontology seeks to support various data integration needs of enzyme biotechnology from inception to product roll. Serving as a knowledgebase for decision support, the conceptualization seeks to link fungal species with enzymes, enzyme substrates, enzyme classifications, enzyme modifications, enzyme related intellectual property, enzyme retail and applications. The ontology, developed in the OWL language, is the result of the integration of numerous biological database schemas, web accessible text resources and components of existing ontologies. We assess the quantity of implicit knowledge in the FungalWeb Ontology by analyzing the range of tags in the OWL files and along with other description logic (DL) computable metrics of the ontology, contrast it with other publicly available bio-ontologies. Thereafter, we demonstrate how the FungalWeb Ontology supports its broad remit required in fungal biotechnology by (i) presenting application scenarios (ii) presenting the conceptualizations of the ontological frame able to support these scenarios and (iii) suggesting semantic queries typical of a fungal enzymologist involved in product development. Recognizing the complexity of the ontology query process for the non-technical manager we introduce a simplified query tool, Ontoligent Interactive Query (OntoIQ) that allows the user to browse and build queries from a selection of query patterns and ontology content. The OntoIQ interface supports users not familiar with writing DL syntax allowing them access to the ontology with expressive description logic reasoning tools. Finally we discuss the challenges encountered during the development of semantic infrastructure for fungal enzyme biotechnologists.