Panel: Large Formal Ontologies for Biomedicine A SNOMED Perspective: Start Large, Move Towards Forma

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Panel Large Formal Ontologies for Biomedicine
A SNOMED PerspectiveStart Large, Move Towards
Formal

• Kent A. Spackman, MD, PhD
• Oregon Health Science University, Portland OR
• Chair, SNOMED International Editorial Board

MEDINFO San Francisco September 2004
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Outline

• How large is large?
• How formal is formal?
• Is SNOMED an ontology?
• Is SNOMED an application ontology?
• How long will it take to finish SNOMED?

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How large is large?

• Two answers
• Number of concepts, terms, relationships, etc.
• Difficulty of curation

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It is notoriously difficult to tell what people
mean just by what they say

• From The Economist, Charlemagne column, Sept 4,
  2004
• Decoding a Euro-diplomat takes more than a
  dictionary
• Up to a point means I agree in part? Wrong,
  it means
• No, not in the slightest
• I hear what you say means He accepts my point
  of view? Wrong, it means
• I disagree and do not want to discuss it any
  further
• With the greatest respect means
• I think you are wrong, or a fool
• By the way or incidentally means This is not
  very important? Wrong, it means
• The primary purpose of our discussion is
• Ill bear it in mind ? Ill do nothing about
  it
• Correct me if Im wrong ? Im right, dont
  contradict me

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I don't know what you mean by "glory,"' Alice
said. Humpty Dumpty smiled contemptuously. Of
course you don't -- till I tell you. I meant
"there's a nice knock-down argument for you!"'
But "glory" doesn't mean "a nice knock-down
argument,"' Alice objected. When I use a
word,' Humpty Dumpty said in rather a scornful
tone, it means just what I choose it to mean --
neither more nor less.' The question is,' said
Alice, whether you can make words mean so many
different things.' The question is,' said
Humpty Dumpty, which is to be master - - that's
all.'
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Discerning and representing meaning is extremely
difficult for health terminology

• What is juvenile rheumatoid arthritis?
• Seropositive chronic idiopathic arthritis in
  child lt 16 yrs ?
• Any chronic arthritis in child lt 16 yrs?
• Is Adult-onset Stills disease included?
• Three different published terminology standards,
  all incompatible
• JRA (juvenile rheumatoid arthritis) US
• JCA (juvenile chronic arthritis) UK
• JIA (juvenile idiopathic arthritis)
  International (Edmonton)

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What is the scalp?

• scalp the skin covering the cranium (Stedmans)
• scalp the soft tissue envelope of the cranial
  vault, consists of 5 layers the skin, connective
  tissue, epicranial aponeurosis
  occipitofrontalis muscle, loose areolar tissue,
  and pericranium. (Gardner, Gray ORahilly,
  anatomy text)
• Epicranium (Stedmans) the muscle, aponeurosis
  and skin covering the cranium

It is quite clear SNOMED must have two different
codes (two different Meanings) that bear the name
scalp
We say like Humpty Dumpty When I use the word
scalp,
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What is the fundus?

• To an obstetrician
• To an ophthalmologist
• To a gastrointestinal endoscopist
• To a surgeon doing a lap. cholecystectomy

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What is a pyogenic granuloma?

• Pyogenic pus forming
• Granuloma a collection of inflammatory cells of
  a particular type
• Pyogenic granuloma a benign tumor of small
  blood vessels of the skin
• It is neither pyogenic nor a granuloma.

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What is general paresis?

• General affecting all skeletal muscles
• Paresis weakness
• GPI a form of tertiary neurosyphilis
  characterized by generalized weakness

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How large is large?

• With 800,000 terms in SNOMED CT
• if you spent 5 seconds looking at each one it
  would take you
• 4 million seconds 66,666 minutes 1,111 hours
• 138 work days if thats all you did every day
• 138/5 almost 28 work weeks
• At SNOMED we dont just pretend to know about the
  problems of scale.
• Thats not saying we think weve solved them.

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Content, Content, Content
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Evolutionary Design

• Evolution without pre-ordained design
• Accumulation of desirable features
• Heterogeneity of perspectives
• Dealing with Scale
• Participatory consensus-based approach
• Involve the experts
• Semantics-based concurrency control
• Description logic underpinnings
• Configuration management tools
• Keith Campbells Galapagos tool set

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Formality

• SNOMED is not a formal ontology (but some parts
  of it are migrating in that direction)
• It is a reference terminology that is
  progressively more well-supported by formal
  ontological principles
• Includes terms and non-ontological assertions /
  ideas
• (dare I say concepts?)
• I dislike the term application ontology fish
  or fowl?
• Many of SNOMEDs design decisions are supported
  by formal ontological principles.
• But
• Many of SNOMEDs hierarchies are still
  unprincipled and incomplete.
• Requires continued evolution and maturation

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Regarding violations of good formal ontological
principles in SNOMED

• It may be that it was intentionally designed that
  way
• If intentional, the design may be something we
  need to retain for the sake of URU
• Or it may be something that should be changed
• Or it may be unintentional
• Please dont just assume one way or the other.
  ASK.

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Description Logic Foundation

• SNOMED is based on the description logic known as
  ELH
• Conjunction
• Existential restrictions
• Role hierarchies
• Plus role groups (see 2002 AMIA paper)
• Plus role composition
• So far, only one direct-substance o
  has-active-ingredient

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How long will it take until SNOMED is complete?
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Number of attributes (relationship types) in the
SNOMED concept model
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Percentage of SNOMED CT concept codes that are
fully defined
Eventually should reach 70 or more of
disorders, findings procedures
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SNOMED phases

• 1975-1994 Roger Cote phase
• 1995-1997 Kaiser CMT phase
• 1997-1999 CAP phase building SNOMED RT
• 1999-2002 SNOMED Read merge phase
• 2002-2004 US/UK endorsement phase
• 2004- adoption, use maintenance phase
• The hardest part is still ahead

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There is opportunity to be involved

• Open working group meetings
• Active working groups
• Primary care
• Nursing
• Composition
• Context
• Genomics
• Anesthesiology, pathology, dermatology,
  ophthalmology,
• Dates
• Sept 24, 2004 Phoenix
• Tentative Feb 2, 2005, S. California
• Tentative June 14-15, 2005, Chicago
• Tentative Oct 5, 2005, London