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What is an Ontology? No exact definition A tool to help organize knowledge Or a way to convey a theory on how to represent a class of things Examples of definitions 1 Philosophy Dates back to 5th Century B.C. when Empedocles divided the world into four elements – earth, fire, water and air. – Aristotle, classification Often confused with the word epistomology, which is about knowledge and knowing Defined by philosophers as the nature of being or existence. 2 Webster’s Dictionary Webster’s Third New International Dictionary defines Ontology: 1. A science or study of being specifically, a branch of metaphysics relating to the nature and relations of being. 2. A theory concerning the kinds of entities and specifically the kinds of abstract entities that are to be admitted to a language system. 3 Thomas Gruber “An ontology is a specification of a conceptualization” The conceptualization is an abstract and simplified view of the world you want to represent, which is specified in a format based on the relationships between them. – Examples: hierarchy, cluster, relational diagram 4 The Role of Ontology Basic Role: – To provide a language which allows a group of people to share information reliably in a chosen area of work 5 The Role of Ontology Some areas of application – – – – – – – – Indexing Knowledge Sharing & Reuse Artificial Intelligence (AI) Enterprise Modeling Software Design Molecular Biology eCommerce Semantic Web…. 6 Structure of Ontology Most ontologies are structured as taxonomies or hierarchies Basic ontology has two classes of elements: the entities and the relationships between them (what does this remind you of ?) – Organized according to axioms or rules that control how the world will be defined. 7 Important Facts What exists is only what is represented in the ontology (again like database modeling with entities/relationships) Most ontologies focus on a specific area to conceptualize (e.g. subject thesauri) Must be updated to keep up with dynamic world No set discipline or methodology! 8 Example Biomedical Ontologies GO--Gene Ontology – http://www.geneontology.org/ OBO--Open Biomedical Ontology umbrella web address for well-structured controlled vocabularies for shared use across different biological and medical domains. http://obo.sourceforge.net/ FMA--Foundational Model of Ontologies – http://sig.biostr.washington.edu/projects/fm/Ab outFM.html 9 Tools for working with Ontologies Protégé – http://protege.stanford.edu/ WC3 Web 2.0 tools like – OWL Web Ontology Lanaguage. http://www.w3.org/TR/owl-features/ – RDF Resource Decription Framework http://www.w3.org/RDF/ 10 Further Introduction to BioMedical Ontologies See Barry Smith’s 2 day course notes http://ontology.buffalo.edu/smith/BioOnt ology_Course.html Link to introduction (slides 9-45) 11