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What is an Ontology?

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. Philosophy.

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What is an Ontology?

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  1. 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

  2. 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.

  3. Webster’s Dictionary • Webster’s Third New International Dictionary defines Ontology: • A science or study of being specifically, a branch of metaphysics relating to the nature and relations of being. • A theory concerning the kinds of entities and specifically the kinds of abstract entities that are to be admitted to a language system.

  4. 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

  5. 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

  6. The Role of Ontology • Some areas of application • Indexing • Knowledge Sharing & Reuse • Artificial Intelligence (AI) • Enterprise Modeling • Software Design • Molecular Biology • eCommerce • Semantic Web….

  7. 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.

  8. 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!

  9. 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/AboutFM.html

  10. 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/

  11. Further Introduction to BioMedical Ontologies • See Barry Smith’s 2 day course notes http://ontology.buffalo.edu/smith/BioOntology_Course.html • Link to introduction (slides 9-45)

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