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Ontological analysis of SNOMED CT

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 02.10.2006              Gergely Héja - SMCS2006               1
   Ontological analysis of
        SNOMED CT
             Gergely Héja MSc., György Surján MD., Péter Varga
                                     MSc.
              National Institute for Strategic Health Research,
                             Budapest, Hungary




02.10.2006                    Gergely Héja - SMCS2006             2
                           Aims
    ESKI needs a reference terminology
        To represent of classification systems (ICD,
         ICPM) and public health indicators
        To provide pre co-ordinated code lists for
         enabling semantic interoperability in Hungary
         (and potentially in the EU)
    SNOMED CT seems to be a first choice
    candidate

02.10.2006              Gergely Héja - SMCS2006          3
Needs for classification systems
    Combinatory representation of categories
    based on a reference ontology to enable
        supporting statistical analysis
        formal consistency checking
        (semi)automatic interconnection of different
         classification systems (e.g. ICD and ICPM)
    A high-quality formal ontology is needed,
    but it needs not to be very detailed

02.10.2006              Gergely Héja - SMCS2006         4
             Needs for interoperability
    Detailed common terminology covering the
    whole domain of medicine
    Mapping the concepts of the HIS to the
    concepts of the common terminology and
    vice versa
    A common, consistent, comprehensive
    and decidable ontology is needed


02.10.2006            Gergely Héja - SMCS2006   5
             Computational issues
    Computability vs. comprehensiveness
    Clean hierarchies
    Less emphasis on coverage (the multitude
    of non-defined leaf categories) and greater
    emphasis on rich and well-organized high-
    level categories is needed
    SNOMED CT contains too much concepts


02.10.2006         Gergely Héja - SMCS2006    6
                      Methods
 Based on DOLCE formal top-level ontology
 Review of high and low-level concepts
 needed for the representation of
 classification systems and public health
 indicators
      Is the subsumption relation valid?
      Meaning derived from the FSN vs.
       meaning derived from synonyms vs.
       meaning derived from formal definition
02.10.2006             Gergely Héja - SMCS2006   7
                   Error types - 1
 Misplacing concepts in the hierarchy
        smoker (an agent) is subsumed by tobacco smoking
         behaviour – finding (a role)
        severe asthma is not a kind of asthma, but a kind of
         asthma finding.
 Mixing the subsumption relation with other roles
  (typically part of)
        haemoglobin subsumes haemin (instead of
         constitutional part)
        exacerbation of asthma attack is subsumed by
         asthma (instead of temporal part)

02.10.2006               Gergely Héja - SMCS2006            8
                 Error types - 2
 Hierarchy violating medical thinking and
  biomedical knowledge
        Disease, observation and finding are
         subsumed by clinical finding
        acute on chronic, which is both subsumed by
         acute and chronic
        polycarbonate is a polymer (instead of
         synthetic polymer)


02.10.2006             Gergely Héja - SMCS2006     9
                             Error types - 3
 Contracting disjoint entities into one concept
      Smoker (an agent) and smoker (finding) (a description
       of a situation)
      additional pathologic finding in tumor specimen
       (observable entity) and additional pathologic finding
      Function is classified as an observable entity
              Ontological definition: ability of an object to play a certain role in a certain
              kind of activity
              functions (e.g. gene function, adaptation)
              measures (quality) that evaluate the realisation of a function (e.g.
              respiratory rhythm, excretory rate)
      Inflammation (morphological abnormality) (a physical
       object) and inflammatory reaction (perdurant)

 02.10.2006                           Gergely Héja - SMCS2006                            10
             Additional problems - 1
    Categories taken form classification systems
        pneumonia in other diseases classified elsewhere
         (marked as “ConceptStatus Limited”)
        The danger of taking over concepts from other
         conceptual systems: the context of the concept is lost.
         What is meant by “other diseases classified
         elsewhere”?
    relations (such as part of) are represented also
    as concepts
        It prohibits the direct conversion to any formalism
         based on first order logic, thus to any DL formalism


02.10.2006                Gergely Héja - SMCS2006               11
             Additional problems - 2
 Underspecification:
      roles are not quantified (existential / universal)
      criteria are not specified (necessary / sufficient)
      conversion to DL: do we have to decide in each particular
       case, or can it be done universally?
 Multiple hierarchy
      alcoholic beverage (through its parent ingestible alcohol) is
       subsumed by central depressant, ethyl alcohol and psychoactive
       substance of abuse – non-pharmaceutical. Alcoholic drinks contain
       ethyl alcohol, which plays a role of depressant and substance of
       abuse (with respect to human beings)
      Is this a general phenomenon in SNOMED?
      Which relations are asserted and which are inferred?

02.10.2006                   Gergely Héja - SMCS2006                  12
                  Discussion - 1
    The intended meaning of the categories is
    not always clear: possible translation
    errors
    Is it reasonable to import categories from
    medical classifications?
        Size
        Artificial concepts
        Consistency errors

02.10.2006              Gergely Héja - SMCS2006   13
                  Discussion - 2
    Real world entities listed heterogeneously
        Mars bar and Kit Kat (chocolate candy would
         suffice)
        UFO is subsumed by transport vehicle
        tendon pulley reconstruction is represented,
         but tendon pulley not




02.10.2006             Gergely Héja - SMCS2006          14
                  Solutions
 Use SNOMED as a plain or loosely
  structured list of terms (with extending the
  coverage). Not appropriate for intelligent
  services.
 Restructure SNOMED into a high-quality
  ontology.
 Build a new medical ontology from scratch
  (partial reuse of the existing ones), and to
  restrict   the    use   of    SNOMED        for
  interoperability by mapping concepts to it.

 02.10.2006        Gergely Héja - SMCS2006    15
             Restructuring SNOMED
 A formal top level ontology (e.g. DOLCE).
 A high level core reference ontology of
 general medical knowledge (e.g. anatomy,
 physiology, pathology, medical procedures).
      Logic-based formalism
      Single hierarchies with formal definitions
 (sub)domain ontologies of specialities
      Compound entities (e.g. tonsillitis)
      Manual assertion (e.g. autism)
02.10.2006              Gergely Héja - SMCS2006     16
             Questions?



02.10.2006     Gergely Héja - SMCS2006   17

				
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