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What is an Ontology?

Ontology is a tool to organize knowledge or convey theories on representing classes of things. Learn its history, structure, and applications in various fields. Explore example biomedical ontologies and tools for working with ontologies.

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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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