Queries

Query 1: SPARQL Query to fetch treatments with high effectiveness in patients with the SLC64A-L allele

This query gets all polymorphisms of each gene, then finds the one requested in our competency question, the SLC6A4 long allele (allele name: 5-HTTLPR_L). It then gets all treatment responses that the allele has, all the treatments and their effectivenesses and displays the group of the drugs with the highest effectiveness that exists.

PREFIX pdt: <https://tw.rpi.edu/ontology-engineering/oe2024/personalized-depression-treatment/PersonalizedDepressionTreatment/>

SELECT ?treatment ?effectiveness
WHERE {
  ?gene rdf:type pdt:SLC6A4 .
  FILTER (?gene = pdt:5-HTTLPR_L)
  ?gene pdt:hasResponse ?treatmentResponse .
  ?treatmentResponse pdt:isResponseTo ?treatment .
  ?treatmentResponse pdt:hasTreatmentEffectiveness ?effectiveness .
  BIND(
    IF(?effectiveness = pdt:high, 1,
      IF(?effectiveness = pdt:medium, 2,
        IF(?effectiveness = pdt:low, 3, 4)
      )
    ) AS ?priority
  )
}
ORDER BY ?priority

Result 1: Effective Treatments for SLC64A-L

Treatment	Effectiveness
Citalopram	High
Escitalopram	High
Fluoxetine	High
Fluvoxamine	High
Paroxetine	High
Sertraline	High
Vilazodone	High

Query 2: What treatments are effective against depression in 35 year olds?

This query gets all age based therapeutic indications and the treatments that have the corresponding therapeutic indications. It then checks which therapeutic indications are for groups that contain the age from our competency question (35) in the age range for that group. It then outputs all treatments that match these parameters

PREFIX pdt: <https://tw.rpi.edu/ontology-engineering/oe2024/personalized-depression-treatment/PersonalizedDepressionTreatment/>
PREFIX qv: <https://www.omg.org/spec/Commons/QuantitiesAndUnits/>

SELECT ?treatment
WHERE {
  ?treatment rdf:type/rdfs:subClassOf* pdt:MedicinalProduct .
  ?treatment pdt:hasTherapeuticIndication/pdt:hasTargetPopulation/qv:hasQuantityValueRange/qv:hasLowerBound/rdfs:label ?lowerBound .
  ?treatment pdt:hasTherapeuticIndication/pdt:hasTargetPopulation/qv:hasQuantityValueRange/qv:hasUpperBound/rdfs:label ?upperBound .
  FILTER(xsd:decimal(?upperBound) >= 35 && xsd:decimal(?lowerBound) <= 35)
}

Result 2: Effective treatments for 35 year olds

Treatment Name
Citalopram
Escitalopram
Fluoxetine
Paroxetine
Sertraline

Query 3: What treatments are effective in patients who resist SSRIs?

This query finds all example patients that have shown poor response to the group of SSRIs as the question does not specify specific medications. It then finds the treatment response of the example patient to other treatments. It then outputs the treatments with the best effectiveness and their corresponding effectiveness.

PREFIX pdt: <https://tw.rpi.edu/ontology-engineering/oe2024/personalized-depression-treatment/PersonalizedDepressionTreatment/>

SELECT ?treatment ?effectiveness
WHERE {
  ?patient rdf:type pdt:Patient .
  ?patient pdt:hasResponse ?response .
  FILTER(?response = pdt:SSRI-Low)
  ?treatmentResponse rdf:type pdt:TreatmentResponse .
  ?treatmentResponse pdt:isResponseOf ?patient .
  ?treatmentResponse pdt:hasTreatmentEffectiveness ?effectiveness .
  ?treatmentResponse pdt:isResponseTo ?treatment . 
 BIND(
    IF(?effectiveness = pdt:high, 1,
      IF(?effectiveness = pdt:medium, 2,
        IF(?effectiveness = pdt:low, 3, 4)
      )
    ) AS ?priority
  )
}
ORDER BY ?priority

Result 3: Treatments effective on patients who resist SSRIs

Treatment	Effectiveness
Bupropion	High

Query 4: Which gene alleles impact the effectiveness of SSRIs and what are their impact?

This query finds all gene alleles, finds all the treatments they have responses to, finds the effectiveness of each of those treatments, and then only displays those that are specifically SSRIs

PREFIX pdt: <https://tw.rpi.edu/ontology-engineering/oe2024/personalized-depression-treatment/PersonalizedDepressionTreatment/>

SELECT ?gene ?treatment ?effectiveness
WHERE {
  ?gene rdf:type/rdfs:subClassOf* pdt:Gene .
  ?gene pdt:hasResponse/pdt:isResponseTo ?treatment .
  ?gene pdt:hasResponse/pdt:hasTreatmentEffectiveness ?effectiveness .
  ?treatment rdf:type/rdfs:subClassOf* pdt:SelectiveSerotoninReuptakeInhibitor .
}

Result 4: Effective Treatments for SLC64A-L (Showing 21 out of 100 results)

Gene	Treatment	Effectiveness
SLC6A4-L	Citalopram	High
SLC6A4-L	Escitalopram	High
SLC6A4-L	Fluoxetine	High
SLC6A4-L	Fluvoxamine	High
SLC6A4-L	Paroxetine	High
SLC6A4-L	Sertraline	High
SLC6A4-L	Vilazodone	High
Val66Met_Met	Citalopram	Low
Val66Met_Met	Escitalopram	Low
Val66Met_Met	Fluoxetine	Low
Val66Met_Met	Fluvoxamine	Low
Val66Met_Met	Paroxetine	Low
Val66Met_Met	Sertraline	Low
Val66Met_Met	Vilazodone	Low
rs165599_A	Citalopram	Low
rs165599_A	Escitalopram	Low
rs165599_A	Fluoxetine	Low
rs165599_A	Fluvoxamine	Low
rs165599_A	Paroxetine	Low
rs165599_A	Sertraline	Low
rs165599_A	Vilazodone	Low