Knowledge representation and ontologies for lipids and lipidomics

Abstract

In this thesis, semantic web technologies such as OWL ontology are explored for thepurpose of representing knowledge from the field of lipid research.The first chapter provides a concise background for the field of lipid research, including the emerging area of lipidomics and some of the challenges faced by lipid scientists. The same chapter also provides background on the development of the specific semantic web technologies, followed by a discussion of how these technologies can address some of the challenges identified in lipid research.In the second chapter, the methodology employed to develop ontologies is described.Since there are no standardized methodologies for development of ontologies, the generaldevelopment life cycle and broad principles that are adhered during the development ofontologies for lipids are discussed extensively in this chapter.The third chapter begins with the description of the first Lipid Ontology, namely LipidOntology 1.0. Lipid Ontology 1.0 is a baseline ontology developed to support navigation of information through Knowlegator. Knowlegator is a knowledge visualization tool developed by I2R, A*STAR that enables visualization, navigation and query of knowledge captured in OWL-DL ontologies. This is followed the description of Lipid Ontology Reference and Lipid Ontology Ov.The fourth chapter deals with the description of the Lipid Classification Ontology (LiCO)and Lipid Entity Representation Ontology (LERO). These ontologies are domain orientedontologies that are built for the purpose of representing knowledge formally in OWL-DLand sharing the knowledge with the wider community-the OBO Foundry.The fifth chapter describes an application scenario where the Lipid Ontology is employedin conjunction with a prototype ontology centric content delivery platform(Knowlegator)developed by Institute of Infocomm Research, A*STAR to facilitate knowledge discovery for lipidomics scientists. A preliminary performance analysis of the platform is conducted and the platform is subsequently used to facilitate navigation of pathways.Lastly, the prototype platform is employed to assess the lipidome of ovarian cancer in theliterature.The final chapter contains the concluding remarks for this thesis. A brief summary of the ontologies built during the course of the research is given. The adequacy of OWL-DLontologies as medium of knowledge representation for biological knowledge is re-iterated, specifically for the use case in the knowledge domain of lipids and lipidomics and can be developed into an effective ontology centric application under a platform that is tightly integrated to other technological components of semantic web.