I KNOW JUST WHAT YOUMEAN - ONTOLOGIESAND THEIR USESDave ParryDave.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 saidin rather a scornful tone, `it means justwhat I choose it to mean -- neither mo...
Ontologies   “ Shared understanding of    a conceptualisation”    Deborah L. McGuinness   Controlled set of concepts    ...
What are they for ?   Mapping different terms to the same concept   Search and information retrieval – mapping terms    ...
Why use an Ontology ? example…   Pre-eclampsia   Gestational Proteinuric Hypertension   Toxaemia   GPH   PET   PE  ...
Why standardise ?   Synonyms and obsolescent terms   (HTLVIII vs HIV)   Needed for clinical activity     Communication...
Why use it ?   In EHR systems, to replace/enhance free text.   To support reminders “If patient has allergy to    a drug...
What are they for ?   Mapping different terms to the same concept   Search and information retrieval – mapping    terms ...
Example   Medical ontology    A  finger is “part of” a hand     A hand is “attached to” an arm     Soif your left arm ...
Medical Ontologies               Is a        Limb          Arm                                   Attached to              ...
What are they for ?   Mapping different terms to the same concept   Search and information retrieval – mapping terms    ...
13                         Obstetric     Small Surgical              Which             Forceps ?
What are they for ?   Mapping different terms to the same concept   Search and information retrieval – mapping terms    ...
Systematized Nomenclature ofMedicine-Clinical Terms -SNOMED CT    >600,000K Concepts    SNOMED CT is a clinical vocabula...
SNOMED CT   Very large clinical vocabulary that verges into being    an ontology   Includes Subsets to simplify disambig...
General model                    Extract SNOMED termsUnstructured text                          EHR          Map to ICD 10...
Ontology in ActionOriginal text       Potential                    fragments that                    relate to            ...
Why is coding difficult ?     Experts don’t agree – even when a loose standard     of agreement is required (Chiang 2006)...
So what ?   Errors propagate through systems     SNOMED          >ICD10 >DRG   Free text present in many places in syst...
Cliniclue http://www.clinical-info.co.uk
The semantic web and ontologies   Tim Berners-Lee 2000
OWL – representing ontologies onthe web   Ontology web language    http://www.w3.org/TR/owl-ref/Example :http://owl.man.a...
Designing ontologies   Identify relationships between objects   Relationships depend on domain   Relationships can be s...
Take home message   Ontologies allow real-world    knowledge to be represented    in computer systems   Managing concept...
I know just what you mean - Ontologies and their uses
I know just what you mean - Ontologies and their uses
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I know just what you mean - Ontologies and their uses

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Dave Parry
Auckland University of Technology
(Wednesday, 12.30, Data Analysis Workshop)

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I know just what you mean - Ontologies and their uses

  1. 1. I KNOW JUST WHAT YOUMEAN - ONTOLOGIESAND THEIR USESDave ParryDave.parry@aut.ac.nz
  2. 2. Agenda What is an ontology ? Why use them ? How do you do that ? Where next ?
  3. 3. Words`When I use a word, Humpty Dumpty saidin rather a scornful tone, `it means justwhat I choose it to mean -- neither morenor less.„ Lewis Carroll “Through the LookingGlass – and what Alice found there” Image from “Mathematics Enrichment”
  4. 4. Ontologies “ Shared understanding of a conceptualisation” Deborah L. McGuinness Controlled set of concepts that are themselves linked by concepts
  5. 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. 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. 7. Why standardise ? Synonyms and obsolescent terms (HTLVIII vs HIV) Needed for clinical activity  Communication  Data analysis  Coding  Reminders etc.
  8. 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. 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. 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. 11. Medical Ontologies Is a Limb Arm Attached to Hand Part of Fingers
  12. 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. 13 Obstetric Small Surgical Which Forceps ?
  14. 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
  15. 15. Systematized Nomenclature ofMedicine-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.
  16. 16. 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.
  17. 17. General model Extract SNOMED termsUnstructured text EHR Map to ICD 10 Send/receive messages
  18. 18. Ontology in ActionOriginal text Potential fragments that relate to SNOMED terms Potential SNOMED Concepts ExpandedSelected Concepts SNOMED Descriptions
  19. 19. 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.
  20. 20. 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)OMalley, 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).
  21. 21. Cliniclue http://www.clinical-info.co.uk
  22. 22. The semantic web and ontologies Tim Berners-Lee 2000
  23. 23. OWL – representing ontologies onthe web Ontology web language http://www.w3.org/TR/owl-ref/Example :http://owl.man.ac.uk/2003/why/latest/
  24. 24. 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”
  25. 25. 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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