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Table 4 Four examples of queries to the patient data

From: Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of cerebrotendinous xanthomatosis

Pattern of CQ Examples of CQ Example of SQWRL Example of answers
What are the genetic variants that have been associated with a combination of traits? What are the genetic variants that have been associated with epilepsy and dementia? Patient(?p) ^ hasNervousSystemDisorder(?p, ?x) ^ Epilepsy(?x) ^ hasPresence(?x, ?y) ^ Yes(?y) ^ hasNervousSystemDisorder(?p, ?d) ^ Dementia(?d) ^ hasPresence(?d, ?y) ^ hasGeneMutation(?p, ?g) ^ GeneticMutation(?g) ^mutation(?g, ?m) → sqwrl:columnNames("GeneMutation") ^ sqwrl:selectDistinct(?m) c.844 + 1 G- > T
p.N403K
p.R395C
p.R405W
p.T339M
p.T343R
What are the abnormalities that have been associated with a specific genetic variant? What are the Abnormalities of the Central Nervous System that have been associated with p.R395C? Patient(?p1) ^ hasNervousSystemDisorder(?p1, ?z) ^ hasPresence(?z, ?y) ^ Yes(?y) ^ AbnormalityoftheCerebellum(?z) ^ hasGeneMutation(?p1, ?g) ˚ sqwrl:makeSet(?s1, ?z) ^ Patient(?p2) ^ hasOtherManifestations(?p2, ?x) ^ hasPresence(?x, ?y) ^ AbnormalityoftheCerebellum(?x) ^ hasGeneMutation(?p2, ?g) ^ sqwrl:makeSet(?s2, ?x) ^ GeneMutation(?g) ^ mutation(?g, ?m) ^ swrlb:equal(?m, "p.R395C") ˚ sqwrl:append(?s3, ?s1, ?s2) ^ sqwrl:element(?e, ?s3) → sqwrl:select(?e) PresenceofAtaxia
PresenceofChiariTypeI
How often has a specific genetic variant been associated with a specific trait? How often has p.R395C been associated with Ataxia? Patient(?p1) ^ hasNervousSystemDisorder(?p1, ?x) ^ Ataxia(?x) ^ hasPresence(?x, ?y) ^ Yes(?y) ^ hasGeneMutation(?p1, ?g) ^ GeneMutation(?g) ^ mutation(?g, ?m) ^ swrlb:equal(?m, "p.R395C") ˚ sqwrl:makeSet(?s1, ?p1) ˚ sqwrl:size(?size1, ?s1) ^ Patient(?p2) ^ hasGeneMutation(?p2, ?g) ^ sqwrl:makeSet(?s2, ?p2) ^ sqwrl:size(?size2, ?s2) ^ swrlb:multiply(?mu, ?size1, 100.0) ^ swrlb:divide(?d, ?mu, ?size2) → sqwrl:select(?d) 57 %
What is the average number of years from the onset of a symptom to the onset of another symptom (or diagnosis/death) in patients with a given genetic variant? What is the average number of years from the onset of diarrhea to the first neurological symptom in patients with the genetic variant p.R395C? Patient(?p1) ^ hasGeneMutation(?p1, ?g) ^ GeneticMutation(?g) ^ mutation(?g, "p.R395C") ^ hasDiarrheaAge(?p1, ?d) ^ AgeatFirstSymptom(?d) ^ age(?d, ?da) ^ hasNeurologicalSymptomsOnsetAge(?p, ?a) ^ AgeatFirstSymptom(?a) ^ age(?a, ?ca) ^ swrlb:subtract(?di, ?ca, ?da) → sqwrl:columnNames("Average age from diarrhea to neurological symptoms onset") ^ sqwrl:avg(?di) 7 years
  1. The first query is about genetic variants associated with a specific combination of observable features; the second query is about phenotype traits associated to a specific genetic variant; and the third and fourth ones are examples of querying information about frequency and elapsed time associated with the presence of a specific genetic variant and trait.