Quick Links
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The National Center for Biomedical OntologyAn international consortium providing a wide range of ontological resources for the biomedical research community.
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NCBO BioPortalA comprehensive repository of biomedical ontologies.
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LHNCBC Medical Ontology Research ProjectBasic research on biomedical terminologies and ontologies and their application. Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine.
What is an Ontology?
When used in computer and information science, the term ontology refers to relationship-based hierarchical descriptions of concepts within a particular domain, such as biomedicine. Ontologies are used within the semantic web to capture a common language for reuse and reapplication in computer systems, improving efficiency and flexibility between systems, and aiding in natural language processing.
Ontologies are used in the biomedical and health sciences in areas ranging from gene function, as seen in the gene ontology GO, to those used in healthcare informatics such as the International Classification of Diseases, ICD.
Introductory Slides and Videos
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Short Introduction to Biological Ontologies, Toni Hermoso Pulido, Centre for Genomic RegulationA short slide introduction to biological ontologies, their relevance, current and future application.
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Introduction to Biomedical Ontologies, Jennifer Smith, Medical College of WisconsinA quick introduction to biomedical ontologies in a series of four 5-10 minute videos.
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Introduction to Biomedical Ontologies, Barry Smith, University of BuffaloA more in-depth series of eight 1-2 hour videos and slides from a two-day course on biomedical ontologies.
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Metadata Standards, Susanna-Assunta Sansone, Oxford UniversityThis one hour video for the BD2K lecture series puts ontologies into the broader context of data standards and interoperability.
Journals
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Applied OntologyAn Interdisciplinary Journal of Ontological Analysis and Conceptual Modeling. (Note: Not available from U-M Library.)
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Journal of Biomedical SemanticsAn open journal addressing issues of semantic enrichment and semantic processing in the biomedical domain.
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Journal of the American Medical Informatics AssociationAMIA's journal for biomedical and health informatics.
Books
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Building Ontologies with Basic Formal Ontology
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ISBN: 9780262527811Publication Date: 2015-07-31An introduction to the field of applied biomedical ontology, covering best practices for ontology design and examples of ontologies in use. The book presents the core features of the Basic Formal Ontology (BFO) with examples, and describes Web Ontology Language (OWL). -
Data Mining Applications Using Ontologies in Biomedicine
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ISBN: 9781596933705Publication Date: 2009-09-01This book describes the theoretical foundations of ontologies, as well as applications of ontologies in biomedicine. -
The Gene Ontology Handbook
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ISBN: 9781493937417Publication Date: 2016-12-02This open access book provides a practical and self-contained overview of the Gene Ontology (GO).
Further Reading
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Bodenreider O. Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support. Yearbook of Medical Informatics. 2008:67-79.A discussion of the practical application of ontologies in the biomedical sciences.
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Gruber T. Ontology. Encyclopedia of Database Systems, Ling Liu and M. Tamer Özsu (Eds.), Springer-Verlag, 2008.A definition of ontology in the context of information science.
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Larsen KR et. al. Behavior Change Interventions: the Potential of Ontologies for Advancing Science and Practice. J Behav Med. 2017 Feb. 40:6-22.An introduction to the use of ontologies in health behavior change interventions.
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Medical Ontology Research - PublicationsA list of publications from the Lister Hill National Center for Biomedical Communications (LHNCBC) Medical Ontology Research Project.
Last Updated: Sep 14, 2022 10:54 AM
Subjects: Health Sciences, Science