Ontologies in Biomedicine What is the

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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

• 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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Porphyrys depiction of Aristotles Categories
Supreme genus SUBSTANCE
Differentiae material immaterial
Subordinate genera BODY SPIRIT
Differentiae animate inanimate
Subordinate genera LIVING
MINERAL
Differentiae sensitive insensitive
Proximate genera ANIMAL PLANT
Differentiae rational irrational
Species HUMAN BEAST
Individuals Socrates Plato Aristotle

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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 Back
ache, unspecified 724.6 Disorders of
sacrum 724.7 Disorders of coccyx 724.70 Unspecif
ied disorder of coccyx 724.71 Hypermobility of
coccyx 724.71 Coccygodynia 724.8 Other symptoms
referable to back 724.9 Other unspecified back
disorders
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The 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 problemsbut 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?