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Exploring OWL Ontology: Medical Ontologies and Disease Treatment Structures

This lecture delves into OWL ontology, exemplifying its structure with medical ontologies, such as UMLS and MeSH. Key concepts include fundamental relationships like hypernymy, membership, and meronymy. The discussion highlights a top-level ontology for disease treatment, illustrating classes such as Disease, Treatment, and Evidence, along with properties and subclasses utilized in medical contexts. Attention is given to OWL document structure, property restrictions, and cardinality aspects, offering a comprehensive understanding of how ontologies inform medical research and practice.

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Exploring OWL Ontology: Medical Ontologies and Disease Treatment Structures

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  1. CS621 : Artificial Intelligence Pushpak BhattacharyyaCSE 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# • 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 • <Quantity> • <Quantityvalue rdf:datatype=float> • 59.5 • </Quantityvalue> • <QuantityUnit rdf:resource=Kilogram> • KG • </ <QuantityUnit> • </Quantity>

  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 • 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 • hasAdministration: AdminsitrationMethod • hasDosage: Dosage

  19. An actual instance of dosage • MDT-1 administration: Drug,Food,Chemicals • Dosage: 109 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

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