Spackman HL7 UK Nov 2004 by hilen

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									 SNOMED Clinical Terms:
Concepts and Descriptions



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




               HL7 UK
       London – November 2004
    Which concepts and which descriptions?

    •   What is SNOMED CT?
    •   What is it for?
    •   How can it be used?
         Relationship to information models, patient data
    •   What is involved in developing & maintaining it?
         Semantics
         Design principles & logic foundation
    •   Opportunities for having input




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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.'
                                       From Through the Looking Glass, Lewis Carrol
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    What is it?

    •   “The Systematized Nomenclature of Medicine”




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    What is it?

    •   A reference terminology
    •   A clinical terminology
         with reference and interface properties
    •   A CD containing a set of tables
    •   A set of codes with names
    •   A set of definitions “per genus et differentiam”
    •   A clinical terminology standard
    •   A knowledge base?
    •   A dictionary?
    •   An ontology?
    •   An application ontology?
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    Formal Ontology?

    •   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
           I dislike the term “application ontology” – fish or fowl?

    •   Many of SNOMED’s design decisions are supported by formal
        ontological principles.
          But…
    •   Many of SNOMED’s hierarchies are still “unprincipled” and
        incomplete.
          Requires continued evolution and maturation

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                       SNOMED – CTV3 Timelines
                         SNOMED                      Read Codes

                         SNOMED 2        1979
                                         1980
                                         1981
                                         1982
                                         1983 Read Codes (v1)
                                         1984
                                         1985
                                         1986
                                         1987
                                         1988 Professional Endorsement
                                         1989
                                         1990 Purchased by NHS
                                         1991
                                         1992 Clinical Terms Projects
                         SNOMED 3        1993            “
                                         1994            “
                                         1995 CTV3 (Clinical Terms version 3)
                                         1996 UK Gov’t Inquiries into Read Codes
                       CAP business plan 1997           “
    Formation of the
       SNOMED
                                         1998           “
      International    NHS Agreement     1999 CAP Agreement
     Division of the     SNOMED RT       2000
         C.A.P.
                                         2001
                                         2002
                                 SNOMED Clinical Terms
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    SNOMED CT Releases

      1st   Jan 31, 2002
      2nd   July 31, 2002
      3rd   Jan 31, 2003
      4th   July 31, 2003
      5th   Jan 31, 2004
      6th   July 31, 2004
                    .
                    .
                    .




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    Content, Content, Content




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     Emergence as a Standard:
     Recent Events

     •   Government Actions – US and UK
            US National License
            ANSI – Terminology Distribution Structure Standard
            US NCVHS – HIPAA recommendation
            US Government CHI Initiative recommendation
            UMLS release
            UK NPfIT adoption




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     What does it do?


     •   SNOMED CT is a terminological resource that can
         be implemented in software applications to
         represent clinically relevant information
          In a “semantically structured” form that can be used
           by automated applications




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     What is it for?

     •   It is for building applications capable of:
          Recording statements about the health and health
           care of individuals
             • In a way that permits retrieval according to the
               meaning of the statements, rather than just the words
               used
          Retrieving individual cases and groups of cases
             • To enable more automated and sophisticated
               decision support, epidemiology, and research




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     Successful use of SNOMED CT depends on:

     •   Implementation in clinical records systems

     •   Which in turn requires (at least) a patient data
         model (information model)




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      The simplest information model

     •    Put all clinical data here ___________________




     The simplest terminology model

      •   Two values:
           • Yes
           • No

     Intermediate between these extremes there are many possible solutions!


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     What about clinical decision support?




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     What about clinical decision support?

      IF Two blood cultures, drawn through
      an antibiotic removal device, more
        than 30 minutes apart,
        grow no organism,
      THEN discontinue antibiotic.




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                procedures




        IF Two blood cultures, drawn through
        an antibiotic removal device, more
          than 30 minutes apart,
          grow no organism,            finding

        THEN discontinue antibiotic.
     device




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           Clinical Decision Support Model
                   + Inference Rules




     Terminology Model                                Information Model
        + Coded Data                               + Patient Data Structures




                         Diagram based on Figure 1 in Rector AL et al. “Interface of Inference Models with
18                       Concept and Medical Record Models” AIME 2001: 314-323
                    Clinical Decision Support Model
                            + Inference Rules
                                                                           IF Two blood cultures, drawn through
                                                                           Antibiotic removal device, more
                                                                           than 30 minutes apart, grows no organism,
                                                                           THEN discontinue antibiotic.




     SNOMED CT                                                                                       HL7 RIM

      Terminology Model                                                        Information Model
         + Coded Data                                                       + Patient Data Structures
       30088009    blood culture                                                What test was performed?
       55512120    antibiotic removal device                                    How many were done?
       264868006   No growth                                                    At what time?
       281789004    antibiotic therapy                                          What device was used?
       223438000   advice to discontinue a procedure                            What was the result of the test?


                                                  Diagram based on Figure 1 in Rector AL et al. “Interface of Inference Models with
19                                                Concept and Medical Record Models” AIME 2001: 314-323
     What is involved in creating and maintaining
     SNOMED CT?

     •   Representation of meaning
          Judgments of “same or different”
          Representing clearly “what clinicians mean when
           they say …”




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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 …”
           “I’ll bear it in mind”  “I’ll do nothing about it”
           “Correct me if I’m wrong”  “I’m right, don’t contradict me”

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     Discerning and representing meaning of
     health terminology is difficult
     •   What is juvenile rheumatoid arthritis?
          Seropositive chronic idiopathic arthritis in child < 16
           yrs ?
          Any chronic arthritis in child < 16 yrs?
          Is Adult-onset Still’s disease included?

     •   Three different published terminology standards,
         all incompatible
          JRA (juvenile rheumatoid arthritis) – US
          JCA (juvenile chronic arthritis) – UK
          JIA (juvenile idiopathic arthritis) – International


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     Words alone are insufficient
     •   There are national, regional and local variations in meaning of
         words and phrases (even within the same language)
     •   Multiple meanings with the same “preferred name”
     •   Combining words gives something entirely different from the sum of
         the parts
     •   Ambiguous shorthand and abbreviations are common
     •   The same phrase means different things to different specialists
     •   The same word or phrase means different things depending on what
         you are doing at the time
     •   Significant differences in meaning are often obscured through use of
         the same word
     •   Formal definitions are often at variance with common clinical usage
     •   A general name takes on a more specific meaning
     •   A manifestation is often used to name the disorder in which it occurs
     •   Successful communication relies on making ontological distinctions
         that are ignored by common phrasing

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     What is “pudding”?

     •   At dinner in Phoenix, Roger (from the UK) asked
         “Is anyone having pudding?”
     •   To which I replied, “Do you mean dessert?”
     •   And he said, “No, I mean pudding.”




                                 ?
     Within the same language there are significant national, regional
     and local variations
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     What is “scalp”?

     •   scalp: the skin covering the cranium (Stedman’s)
     •   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 & O’Rahilly, anatomy text)
     •   Epicranium (Stedman’s): 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 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.




     Combinations are frequently very different from the sum of their parts

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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




     Shorthand and abbreviations are common

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     What is “acute inflammation”?

     •   To the GP, it is inflammation with an acute onset,
         characterised by redness, heat, swelling and pain.

     •   To the pathologist, it is inflammation in which
         polymorphonuclear leukocytes predominate, as
         opposed to chronic inflammation, in which
         “mononuclear cells” (lymphocytes, plasma cells,
         monocytes, histiocytes) predominate.



     The same phrase can mean different things to different specialists

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     What is the “fundus”?

     •   When caring for a pregnant patient –

     •   When examining the eyes –

     •   When doing a gastroscopy –

     •   When doing a cholecystectomy –




     What you are doing at the time changes the meaning of words

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     Is there an error in this hierarchy?



     Radiographic procedures
        Angiography procedures
            Magnetic resonance angiography procedures




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     Is there an error in this hierarchy?



     Radiographic procedures
        Angiography procedures
            Magnetic resonance angiography procedures




     It is common for a general name to acquire a more specific meaning

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     Is there an error in this hierarchy?


          psoriasis
             psoriasis with arthropathy
                juvenile psoriatic arthritis
                    juvenile psoriatic arthritis without psoriasis




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     Is there an error in this hierarchy?


             psoriasis
                psoriasis with arthropathy
                   juvenile psoriatic arthritis
                       juvenile psoriatic arthritis without psoriasis




     It is common for the disorder to be named by its manifestation

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     What is a “laceration”?

     •   Torn or jagged wound
             vs
     •   Accidental cut wound


     •   Perineal laceration during O-P delivery
             vs
     •   Laceration of thumb while using kitchen knife



     Subtle distinctions are often implicit

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     What is the “leg”?

     •   1) same as “lower limb”
     •   2) just the part from the knee to the ankle
          Stedman’s “the segment of the inferior limb between
           the knee and the ankle”
          Dorland’s “that section of the lower limb between the
           knee and ankle”




     Some formal definitions are in conflict with ordinary usage

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     What does “aspirin” mean?

     •   Some aspirin – the chemical ASA
     •   An aspirin – a tablet containing ASA




     Formal ontologists insist on a clean distinction between the individual
     and the matter or stuff of which it is made.
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     How does SNOMED address these issues?

     •   Careful representation of meaning
          Evolutionary design
          Formal description logic foundation
          Consensus process
             • URU criteria: understandable, reproducible, useful




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     We are not the language police




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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 Campbell’s “Galapagos” tool set

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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 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 that’s all you did every day
          138/5 = almost 28 work weeks


     •   At SNOMED we don’t just pretend to know about
         the problems of scale.
     •   That’s not saying we think we’ve solved them.


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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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     How long will it take?

     •   That depends on what you want:
          It is ready for use now.
          If you wait for perfection you wait forever.
          But tell us what needs the most urgent attention.




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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 + on-line discussion forums
     •   Active working groups:
           Concept model working group
           Mapping working group
           Content-area focused working groups
             •   Primary care
             •   Nursing
             •   Genomics
             •   Anesthesiology, pathology, dermatology, ophthalmology, …
     •   Upcoming in-person meeting dates:
           Feb 2, 2005, S. California
           June 14-15, 2005, Chicago
           Oct 5, 2005, London

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     Concept Model Working Group issues:

     •   Context
     •   Negation
     •   Composition (“post-coordination”)
     •   Interface between concept model & information
         model
          Specifically interface between SNOMED & HL7 v3
          Proposed work item (or possible SIG) with HL7
           vocab




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