Scenario 1: Genetic Analysis Case Study on FBX011 gene.

Scenario 1: Genetic Analysis Case Study on FBX011 gene.#

An Undiagnosed Child with Mental Retardation and Facial Dysmorphisms#

An undiagnosed child with mental retardation and facial dysmorphisms, with a negative array-CGH analysis, underwent Whole Exome Sequencing (WES). This disclosed a de novo, likely pathogenic, rare variant in the FBX011 gene.

Research Questions#

Question 1: Gene-Disease Relationship#

Is there a relationship between the FBX011 gene mutation and the observed disease?

Work in Progress: This query is still under development and may not yet provide complete or accurate results. It serves as a foundation for further refinement and enhancement. 
PREFIX sio: <http://semanticscience.org/ontology/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX caresm: <http://example.com/caresm/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?gene ?geneLabel ?mutation ?disease
WHERE {
  # Identify the gene associated with the mutation
  ?gene rdf:type sio:SIO_000115 ;  # Identifier for the gene
        rdfs:label "FBX011"@en .

  # Find the mutation associated with the gene
  ?mutation rdf:type sio:SIO_000115 ;  # Identifier for the mutation
           sio:denotes ?gene .

  # Find the individual related to the mutation and disease
  ?individual rdf:type sio:SIO_000498 ;  # Individual
              sio:denotes ?mutation ;
              sio:has-role ?role .

  # Find the role realized in a process
  ?role rdf:type sio:SIO_000016 ;
        sio:realized-in ?process .

  # Find the process overlapping with a specific process and related to disease
  ?process rdf:type sio:SIO_000006 ;
           sio:overlaps-with ?specific_process ;
           sio:has-input ?input ;
           sio:has-target ?disease ;
           sio:has-output ?output .

  # Find the specific process, input, and output related to the process
  ?specific_process rdf:type sio:SIO_000006 .
  ?input rdf:type sio:SIO_000015 .
  ?disease rdf:type sio:SIO_000015 ;  # Disease
            rdfs:label ?diseaseLabel .
  ?output rdf:type sio:SIO_000015 .

  # Ensure the labels are in English
  FILTER(LANG(?diseaseLabel) = "en") .
}

Question 2: Mutation Prevalence#

Are there any other individuals with the mutation or allelic variant?

Work in Progress: This query is still under development and may not yet provide complete or accurate results. It serves as a foundation for further refinement and enhancement. 
PREFIX sio: <http://semanticscience.org/ontology/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX caresm: <http://example.com/caresm/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?individual ?individualLabel
WHERE {
  # Identify the mutation of interest
  ?mutation rdf:type sio:SIO_000115 ;
            rdfs:label "FBX011_mutation"@en .

  # Find individuals with the same mutation
  ?individual rdf:type sio:SIO_000498 ;  # Individual
              sio:denotes ?mutation ;
              rdfs:label ?individualLabel .

  # Ensure the labels are in English
  FILTER(LANG(?individualLabel) = "en") .
}

Question 3: Phenotype and Prognosis#

If there are, what is their phenotype? What can be derived from them for the prognosis?

Work in Progress: This query is still under development and may not yet provide complete or accurate results. It serves as a foundation for further refinement and enhancement. 
PREFIX sio: <http://semanticscience.org/ontology/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX caresm: <http://example.com/caresm/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?individual ?individualLabel ?phenotype ?phenotypeLabel ?prognosis ?prognosisLabel
WHERE {
  # Identify the gene of interest
  ?gene rdf:type sio:SIO_000115 ;
        rdfs:label "FBX011"@en .

  # Find mutations associated with the gene
  ?mutation rdf:type sio:SIO_000115 ;
            sio:denotes ?gene .

  # Find individuals with these mutations
  ?individual rdf:type sio:SIO_000498 ;  # Individual
              sio:denotes ?mutation ;
              rdfs:label ?individualLabel .

  # Find the phenotype of these individuals
  ?individual sio:has-attribute ?phenotype .
  ?phenotype rdf:type sio:SIO_000614 ;  # Phenotype
             rdfs:label ?phenotypeLabel .

  # Find the prognosis related to these individuals
  ?individual sio:has-attribute ?prognosis .
  ?prognosis rdf:type sio:SIO_000614 ;  # Prognosis
             rdfs:label ?prognosisLabel .

  # Ensure the labels are in English
  FILTER(LANG(?individualLabel) = "en") .
  FILTER(LANG(?phenotypeLabel) = "en") .
  FILTER(LANG(?prognosisLabel) = "en") .
}

Question 4: Variant Frequency in Populations#

What is the variant frequency across different populations?

Work in Progress: This query is still under development and may not yet provide complete or accurate results. It serves as a foundation for further refinement and enhancement. 
PREFIX sio: <http://semanticscience.org/ontology/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX caresm: <http://example.com/caresm/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?population ?populationLabel ?mutation ?mutationLabel ?frequency ?frequencyLabel
WHERE {
  # Identify the mutation of interest
  ?mutation rdf:type sio:SIO_000115 ;  # Identifier
            rdfs:label "FBX011_mutation"@en ;
            sio:denotes ?gene .

  # Find populations with this mutation
  ?observation rdf:type sio:SIO_000498 ;  # Observation
               sio:has-input ?mutation ;
               sio:has-output ?frequency ;
               sio:has-agent ?population .

  # Get the labels for the mutation, frequency, and population
  ?mutation rdfs:label ?mutationLabel .
  ?frequency rdf:type sio:SIO_001367 ;  # Frequency
             rdfs:label ?frequencyLabel .
  ?population rdf:type sio:SIO_000015 ;  # Population
              rdfs:label ?populationLabel .

  # Ensure the labels are in English
  FILTER(LANG(?mutationLabel) = "en") .
  FILTER(LANG(?frequencyLabel) = "en") .
  FILTER(LANG(?populationLabel) = "en") .
}
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