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I KNOW JUST WHAT YOU
MEAN - ONTOLOGIES
AND THEIR USES
Dave Parry
Dave.parry@aut.ac.nz
Agenda
   What is an ontology ?
   Why use them ?
   How do you do that ?
   Where next ?
Words

`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.„
  Lewis Carroll “Through the Looking
Glass – and what Alice found there”




                Image from “Mathematics Enrichment”
Ontologies
   “ Shared understanding of
    a conceptualisation”
    Deborah L. McGuinness
   Controlled set of concepts
    that are themselves linked
    by concepts
What are they for ?
   Mapping different terms to the same concept
   Search and information retrieval – mapping terms
    to concepts that are broader or narrower
   Disambiguation – deciding WHICH concept you
    mean
   Finding and converting concepts – especially for
    coding
Why use an Ontology ? example…

   Pre-eclampsia
   Gestational Proteinuric Hypertension
   Toxaemia
   GPH
   PET
   PE
   All the same all map to.. pre-eclampsia 398254007 -
    code
Why standardise ?
   Synonyms and obsolescent terms
   (HTLVIII vs HIV)
   Needed for clinical activity
     Communication

     Data analysis
     Coding

     Reminders etc.
Why use it ?
   In EHR systems, to replace/enhance free text.
   To support reminders “If patient has allergy to
    a drug code recorded then alert if drug is being
    prescribed”
   Converting free text to coded data….
What are they for ?
   Mapping different terms to the same concept
   Search and information retrieval – mapping
    terms to concepts that are broader or narrower
   Disambiguation – deciding WHICH concept
    you mean
   Finding and converting concepts – especially
    for coding
Example
   Medical ontology
    A  finger is “part of” a hand
     A hand is “attached to” an arm



     Soif your left arm is amputated – the fingers are not
     present on that side of the body !
Medical Ontologies

               Is a


        Limb          Arm

                                   Attached to

                            Hand

                                   Part of

                              Fingers
What are they for ?
   Mapping different terms to the same concept
   Search and information retrieval – mapping terms
    to concepts that are broader or narrower
   Disambiguation – deciding WHICH concept you
    mean
   Finding and converting concepts – especially for
    coding
13
                         Obstetric
     Small Surgical




              Which
             Forceps ?
What are they for ?
   Mapping different terms to the same concept
   Search and information retrieval – mapping terms
    to concepts that are broader or narrower
   Disambiguation – deciding WHICH concept you
    mean
   Finding and converting concepts – especially for
    coding
I know just what you mean - Ontologies and their uses
Systematized Nomenclature of
Medicine-Clinical Terms -
SNOMED CT

    >600,000K Concepts
    SNOMED CT is a clinical vocabulary currently
     administered by the international health terminology
     standards development organisation (IHTSDO)
     http://www.ihtsdo.org/. Member countries are;
     Australia, Canada, Denmark, Lithuania, The
     Netherlands, New Zealand, Sweden, United Kingdom
     and United States.
SNOMED CT
   Very large clinical vocabulary that verges into being
    an ontology
   Includes Subsets to simplify disambiguation and
    reduce search space
   Mapping between SNOMED concepts and clinical
    coding already exists.
General model

                    Extract SNOMED terms



Unstructured text                          EHR




          Map to ICD 10        Send/receive messages
Ontology in Action
Original text       Potential
                    fragments that
                    relate to
                    SNOMED terms




                                     Potential
                                     SNOMED
                                     Concepts




                    Expanded
Selected Concepts   SNOMED
                    Descriptions
Why is coding difficult ?
     Experts don’t agree – even when a loose standard
     of agreement is required (Chiang 2006)
    SNOMED CT is very large and changes by 5-10%
     each release
     Data is used in ways that might be unfamiliar to
     the originator
    Ontologies can help resolve the meaning

    Reliability of SNOMED-CT Coding by Three Physicians using Two Terminology Browsers
    Michael F. Chiang, John C. Hwang, Alexander C. Yu, Daniel S. Casper, James J. Cimino, and Justin Starren
    AMIA Annu Symp Proc. 2006; 2006: 131–135.
So what ?
   Errors propagate through systems
     SNOMED          >ICD10 >DRG
   Free text present in many places in systems.
   Systems supporting coding may do better in
    avoiding “Paper trail” errors (O’Malley 2005)

O'Malley, K. J., Cook, K. F., Price, M. D., Wildes, K. R., Hurdle, J. F., & Ashton, C. M.
   (2005). Measuring diagnoses: ICD code accuracy.(International Classification of
   Diseases). Health Services Research, 40(5), 1620(1620).
Cliniclue http://www.clinical-
info.co.uk
I know just what you mean - Ontologies and their uses
The semantic web and ontologies

   Tim Berners-Lee 2000
OWL – representing ontologies on
the web
   Ontology web language
    http://www.w3.org/TR/owl-ref/

Example :
http://owl.man.ac.uk/2003/why/latest/
Designing ontologies
   Identify relationships between objects
   Relationships depend on domain
   Relationships can be simple “is-a” or extremely
    complex e.g. “happens after all of the previous
    events”
Take home message
   Ontologies allow real-world
    knowledge to be represented
    in computer systems
   Managing concepts is a key
    task of health informatics
   The semantic web allows us
    to store knowledge on the
    web – and even move to
    wisdom on the web

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I know just what you mean - Ontologies and their uses

  • 1. I KNOW JUST WHAT YOU MEAN - ONTOLOGIES AND THEIR USES Dave Parry Dave.parry@aut.ac.nz
  • 2. Agenda  What is an ontology ?  Why use them ?  How do you do that ?  Where next ?
  • 3. Words `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.„ Lewis Carroll “Through the Looking Glass – and what Alice found there” Image from “Mathematics Enrichment”
  • 4. Ontologies  “ Shared understanding of a conceptualisation” Deborah L. McGuinness  Controlled set of concepts that are themselves linked by concepts
  • 5. What are they for ?  Mapping different terms to the same concept  Search and information retrieval – mapping terms to concepts that are broader or narrower  Disambiguation – deciding WHICH concept you mean  Finding and converting concepts – especially for coding
  • 6. Why use an Ontology ? example…  Pre-eclampsia  Gestational Proteinuric Hypertension  Toxaemia  GPH  PET  PE  All the same all map to.. pre-eclampsia 398254007 - code
  • 7. Why standardise ?  Synonyms and obsolescent terms  (HTLVIII vs HIV)  Needed for clinical activity  Communication  Data analysis  Coding  Reminders etc.
  • 8. Why use it ?  In EHR systems, to replace/enhance free text.  To support reminders “If patient has allergy to a drug code recorded then alert if drug is being prescribed”  Converting free text to coded data….
  • 9. What are they for ?  Mapping different terms to the same concept  Search and information retrieval – mapping terms to concepts that are broader or narrower  Disambiguation – deciding WHICH concept you mean  Finding and converting concepts – especially for coding
  • 10. Example  Medical ontology A finger is “part of” a hand  A hand is “attached to” an arm  Soif your left arm is amputated – the fingers are not present on that side of the body !
  • 11. Medical Ontologies Is a Limb Arm Attached to Hand Part of Fingers
  • 12. What are they for ?  Mapping different terms to the same concept  Search and information retrieval – mapping terms to concepts that are broader or narrower  Disambiguation – deciding WHICH concept you mean  Finding and converting concepts – especially for coding
  • 13. 13 Obstetric Small Surgical Which Forceps ?
  • 14. What are they for ?  Mapping different terms to the same concept  Search and information retrieval – mapping terms to concepts that are broader or narrower  Disambiguation – deciding WHICH concept you mean  Finding and converting concepts – especially for coding
  • 16. Systematized Nomenclature of Medicine-Clinical Terms - SNOMED CT  >600,000K Concepts  SNOMED CT is a clinical vocabulary currently administered by the international health terminology standards development organisation (IHTSDO) http://www.ihtsdo.org/. Member countries are; Australia, Canada, Denmark, Lithuania, The Netherlands, New Zealand, Sweden, United Kingdom and United States.
  • 17. SNOMED CT  Very large clinical vocabulary that verges into being an ontology  Includes Subsets to simplify disambiguation and reduce search space  Mapping between SNOMED concepts and clinical coding already exists.
  • 18. General model Extract SNOMED terms Unstructured text EHR Map to ICD 10 Send/receive messages
  • 19. Ontology in Action Original text Potential fragments that relate to SNOMED terms Potential SNOMED Concepts Expanded Selected Concepts SNOMED Descriptions
  • 20. Why is coding difficult ?  Experts don’t agree – even when a loose standard of agreement is required (Chiang 2006)  SNOMED CT is very large and changes by 5-10% each release  Data is used in ways that might be unfamiliar to the originator  Ontologies can help resolve the meaning Reliability of SNOMED-CT Coding by Three Physicians using Two Terminology Browsers Michael F. Chiang, John C. Hwang, Alexander C. Yu, Daniel S. Casper, James J. Cimino, and Justin Starren AMIA Annu Symp Proc. 2006; 2006: 131–135.
  • 21. So what ?  Errors propagate through systems  SNOMED >ICD10 >DRG  Free text present in many places in systems.  Systems supporting coding may do better in avoiding “Paper trail” errors (O’Malley 2005) O'Malley, K. J., Cook, K. F., Price, M. D., Wildes, K. R., Hurdle, J. F., & Ashton, C. M. (2005). Measuring diagnoses: ICD code accuracy.(International Classification of Diseases). Health Services Research, 40(5), 1620(1620).
  • 24. The semantic web and ontologies  Tim Berners-Lee 2000
  • 25. OWL – representing ontologies on the web  Ontology web language http://www.w3.org/TR/owl-ref/ Example : http://owl.man.ac.uk/2003/why/latest/
  • 26. Designing ontologies  Identify relationships between objects  Relationships depend on domain  Relationships can be simple “is-a” or extremely complex e.g. “happens after all of the previous events”
  • 27. Take home message  Ontologies allow real-world knowledge to be represented in computer systems  Managing concepts is a key task of health informatics  The semantic web allows us to store knowledge on the web – and even move to wisdom on the web