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

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

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

The Foundational Model of AnatomyThe Foundational Model of Anatomy

The NCI Thesaurus in OWL

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A Portion of the OBO Library

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)

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?

The GO is elegant in its simplicity!

But there are clear advantages to having richer semantics

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

What is the “right” amount of semantics?