Ontologies in Biomedicine What is the “right” amount of semantics? Mark A. Musen Stanford...
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Ontologies in BiomedicineWhat is the “right” amount of semantics?
Mark A. Musen
Stanford University
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The National Center for Biomedical Ontology
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• 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
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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
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Supreme genus: SUBSTANCE
Subordinate genera: BODY SPIRIT
Differentiae: material immaterial
Differentiae: animate inanimate
Differentiae: sensitive insensitive
Subordinate genera: LIVING MINERAL
Proximate genera: ANIMAL PLANT
Species: HUMAN BEAST
Differentiae: rational irrational
Individuals: Socrates Plato Aristotle …
Porphyry’s depiction of Aristotle’s Categories
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A Small Portion of ICD9-CM724 Unspecified disorders of the
back724.0 Spinal stenosis, other than
cervical724.00 Spinal stenosis,
unspecified region724.01 Spinal stenosis, thoracic
region724.02 Spinal stenosis, lumbar
region724.09 Spinal stenosis, other724.1 Pain in thoracic spine724.2 Lumbago724.3 Sciatica724.4 Thoracic or lumbosacral neuritis724.5 Backache, unspecified724.6 Disorders of sacrum724.7 Disorders of coccyx724.70 Unspecified disorder of
coccyx724.71 Hypermobility of coccyx724.71 Coccygodynia724.8 Other symptoms referable to back724.9 Other unspecified back disorders
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The Foundational Model of AnatomyThe Foundational Model of Anatomy
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The NCI Thesaurus in OWL
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A Portion of the OBO Library
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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)
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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?
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The GO is elegant in its simplicity!
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But there are clear advantages to having richer semantics
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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
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What is the “right” amount of semantics?