CS621 : Artificial Intelligence

Pushpak BhattacharyyaCSE Dept., IIT Bombay

Lecture 15

OWL ontology: An example

Ontology: Building blocks

Concepts Relationships instances

Fundamental relationships Hypernymy

Subclass (man mammal Membership (Ram ε man)

Meronymy (part whole) (hand part-of body)

Medical Ontologies are famous and elaborate

UMLS, From National Library of Medicine

MeSH (Medical Subject headings (MeSH)

NCI (National Cancer Institute Thesaurus)

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.'

Web ontology language

OWL lite OWL DL OWL full

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

Property restriction Value restrictions

OWL: AllValuesFrom OWL: SomeValuesFrom OWL: hasValue

Cardinality restrictions OWL: minCardinality OWL: maxCardinality OWL: cardinality

Complex classes

Owl: Union Of Owl: IntersectionOf Owl: ComplementOf

Example ontology

An example from NCI: top level ontology of “disease treatment”

Disease-Treatment hasCondition: Condition hasTreatment: Treatment hasDisease: Disease hasEffect: Effect hasEvidence: Evidence

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

Properties associated with disease

hasLocationAnatomy (equated with Anatomic Structure, System or Substance)

hasSizeQuantity hasDurationQuantity atStageDiseaseStage

Quantity class

<Quantity> <Quantityvalue rdf:datatype=float>

59.5 </Quantityvalue> <QuantityUnit rdf:resource=Kilogram>

KG </ <QuantityUnit>

</Quantity>

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

Treatment Class link

Two subproperties hasPrimaryTreatment and hasSeconderyTreatment

Subclasses Chemotherapy Regimen Drug, Food. Chemical or Biomedical

Material Intervention or Procedure

Two general properties of the treatment class

HasfrequencyAdminstrationFrequency (3 times a day, every 4 hours etc.)

hasDuration AdminsitrationDuration (10 days, one month etc.)

Properties of Drug, Food and Chemicals class link

hasAdministration: AdminsitrationMethod

hasDosage: Dosage

An actual instance of dosage

MDT-1 administration: Drug,Food,Chemicals Dosage: 109 cfu AdministrationFrequency: 3 times a

week AdministrationDuration: 4 weeks

The Effect Class atTImeTemporalObject (how long after the treatment does

the effect occur) hasMeasurementMethodMeasurementMethod hasModalityModality (degree of confidence “posible”,

“probable”, “unlikely” etc.) hasEffectObjectEfffectObject (the object upon which the

effect occurs, e.g., “skin”) hasObjectAttributeObjectAttribute (the specific attribute

being effected, e.g., “colour”) hasEffectTypeEffectType (e.g. “reduce”, “inhibit”, “prevent”,

“remove”) hasEffectvalueEffectValue( specifies the direction and extent

of the effect) hasEvidenceEvidence (to link the details of the research

study and results)

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)

Evidence class Providedby Organization (e.g., NIMH) hasResearchLocationLocation (e.g., TMH,

Mumbai) hasResearchTypeResearchType (e.g.,

systematic review, randomized control trial, animal studies etc.)

hasExperimentalSubject ExperimentalSubject (e.g., person, mouse etc.)

hasSampleSizeQuantity hasDurationTemporalQuantityQuantity

Automation effort

Extarction by a program from Medical Abstracts

Research at NTU, Signapore uner Prof. Christopher Khoo