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Ontologies in Biomedicine What is the “right” amount of semantics?

This article discusses the importance of developing ontologies in biomedicine to facilitate information sharing, reuse of domain knowledge, and interoperability. It explores different dimensions for characterizing ontologies and the paradox of balancing simplicity with rich semantics. The panelists provide insights on determining the optimal level of semantics in ontologies.

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Ontologies in Biomedicine What is the “right” amount of semantics?

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  1. Ontologies in BiomedicineWhat is the “right” amount of semantics? Mark A. Musen Stanford University

  2. The National Center for Biomedical Ontology • One of three National Centers for Biomedical Computing launched by NIH in 2005 • Collaboration of Stanford, Berkeley, Mayo, Buffalo, Victoria, UCSF, Oregon, and Cambridge • Primary goal is to make ontologies accessible and usable • Research will develop technologies for ontology indexing, alignment, and peer review

  3. Why Develop an Ontology? • To share common understanding of the structure of descriptive information • among people • among software agents • between people and software • To enable reuse of domain knowledge • to avoid “re-inventing the wheel” • to introduce standards to allow interoperability

  4. Porphyry’s depiction of Aristotle’s Categories Supreme genus:SUBSTANCE Differentiae: material immaterial Subordinate genera:BODYSPIRIT Differentiae: animate inanimate Subordinate genera:LIVINGMINERAL Differentiae: sensitive insensitive Proximate genera:ANIMALPLANT Differentiae: rational irrational Species:HUMANBEAST Individuals:Socrates Plato Aristotle …

  5. A Small Portion of ICD9-CM 724 Unspecified disorders of the back 724.0 Spinal stenosis, other than cervical 724.00 Spinal stenosis, unspecified region 724.01 Spinal stenosis, thoracic region 724.02 Spinal stenosis, lumbar region 724.09 Spinal stenosis, other 724.1 Pain in thoracic spine 724.2 Lumbago 724.3 Sciatica 724.4 Thoracic or lumbosacral neuritis 724.5 Backache, unspecified 724.6 Disorders of sacrum 724.7 Disorders of coccyx 724.70 Unspecified disorder of coccyx 724.71 Hypermobility of coccyx 724.71 Coccygodynia 724.8 Other symptoms referable to back 724.9 Other unspecified back disorders

  6. The Foundational Model of Anatomy

  7. The NCI Thesaurus in OWL

  8. A Portion of the OBO Library

  9. Some dimensions for characterizing ontologies • Large vs. Small (e.g., FMA vs. SOFG Anatomy Entry List) • Broad vs. Deep (e.g., UMLS Semantic Network vs. CYC) • “Lite” vs. Heavy (e.g., Gene Ontology vs. FMA)

  10. The fundamental paradox • GO and other ontologies became popular because they assumed a simple semantics that required little of developers • The lack of rich semantics has enabled errors to creep into ontologies such as GO and the meaning of terms and relations to drift • Many ontology developers are now turning to rich representation formalisms (e.g., OWL) to overcome these problems—but are they shooting themselves in the foot by doing do?

  11. The GO is elegant in its simplicity!

  12. But there are clear advantages to having richer semantics

  13. Our distinguished panelists • Christopher Chute, Professor and Chair, Department of Medical Informatics, the Mayo Clinic • Suzanna Lewis, Senior Staff Scientist, Lawrence Berkeley National Laboratory • Barry Smith, Professor of Philosophy, University at Buffalo

  14. What is the “right” amount of semantics?

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