1. CS621 : Artificial Intelligence Pushpak Bhattacharyya CSE Dept., IIT Bombay Lecture 15 OWL ontology: An example

2. Ontology: Building blocks Concepts Relationships instances

3. Fundamental relationships Hypernymy Subclass (man mammal Membership (Ram ε man) Meronymy (part whole) (hand part-of body)

4. Medical Ontologies are famous and elaborate UMLS, From National Library of Medicine MeSH (Medical Subject headings (MeSH) NCI (National Cancer Institute Thesaurus)

5. UMLS semantic n/w Major groupings of semantic types include organisms, anatomical structures, biologic function, chemicals, events, physical objects, and concepts or ideas. Is-a hierarchy Non-hierarchical relations:`physically related to,' `spatially related to,' `temporally related to,' `functionally related to,' and `conceptually related to.'

6. Web ontology language OWL lite OWL DL OWL full

7. Structure of OWL document Name space http://www.w3.org/2002/07/owl# http://www.w3.org/2002/07/owl# Name Space name owl OWL header: version information, ontology comments, import statements, title, creator etc. Owl:imports used to import other ontologies

8. Property restriction Value restrictions OWL: AllValuesFrom OWL: SomeValuesFrom OWL: hasValue Cardinality restrictions OWL: minCardinality OWL: maxCardinality OWL: cardinality

9. Complex classes Owl: Union Of Owl: IntersectionOf Owl: ComplementOf

10. Example ontology

11. An example from NCI: top level ontology of “disease treatment” Disease-Treatment hasCondition: Condition hasTreatment: Treatment hasDisease: Disease hasEffect: Effect hasEvidence: Evidence

12. Disease class Equated to Disease, Disorder or finding Class Disease, Disorder or finding Disease or Disorder Behaviour disorder Cancer condition Disorder by site Genetic disorder Hamartoma Neoplasm Neoplasm by site Neoplasm by morphology polyp Finding

13. Properties associated with disease hasLocation  Anatomy (equated with Anatomic Structure, System or Substance) hasSize  Quantity hasDuration  Quantity atStage  DiseaseStage

14. Quantity class 59.5 KG

15. Anatomic Structure, System or Substance class Anatomic Structure, System or Substance Body cavity Body Fluid or substance Body Part Anatomic Surface Cardiovascular System Cell part Fossa Gastrointestinal System part Anterior surface of stomach Antrum Pylori Appendix

16. Treatment Class link link Two subproperties hasPrimaryTreatment and hasSeconderyTreatment Subclasses Chemotherapy Regimen Drug, Food. Chemical or Biomedical Material Intervention or Procedure

17. Two general properties of the treatment class Hasfrequency  AdminstrationFrequency (3 times a day, every 4 hours etc.) hasDuration  AdminsitrationDuration (10 days, one month etc.)

18. Properties of Drug, Food and Chemicals class link link hasAdministration: AdminsitrationMethod hasDosage: Dosage

19. An actual instance of dosage MDT-1 administration: Drug,Food,Chemicals Dosage: 10 9 cfu AdministrationFrequency: 3 times a week AdministrationDuration: 4 weeks

20. The Effect Class atTIme  TemporalObject (how long after the treatment does the effect occur) hasMeasurementMethod  MeasurementMethod hasModality  Modality (degree of confidence “posible”, “probable”, “unlikely” etc.) hasEffectObject  EfffectObject (the object upon which the effect occurs, e.g., “skin”) hasObjectAttribute  ObjectAttribute (the specific attribute being effected, e.g., “colour”) hasEffectType  EffectType (e.g. “reduce”, “inhibit”, “prevent”, “remove”) hasEffectvalue  EffectValue( specifies the direction and extent of the effect) hasEvidence  Evidence (to link the details of the research study and results)

21. Condition class Three subclasses PatientCondition (age, gender, hasMedicalhistory etc.) DiseaseCondition (presence of disease, e.g., diabetes will indicate a different line of treatment) TreatmentCondition (supportive/optiona/recommended medical environment prior to or during the treatment and includes the property TreatmentHistory, e.g., a certain chemotherapy was done three weeks back)

22. Evidence class Providedby  Organization (e.g., NIMH) hasResearchLocation  Location (e.g., TMH, Mumbai) hasResearchType  ResearchType (e.g., systematic review, randomized control trial, animal studies etc.) hasExperimentalSubject  ExperimentalSubject (e.g., person, mouse etc.) hasSampleSize  Quantity hasDuration  TemporalQuantity  Quantity

23. Automation effort Extarction by a program from Medical Abstracts Research at NTU, Signapore uner Prof. Christopher Khoo