Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: FindSubjectMolecConseqOutput - TTL Representation

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@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <https://loinc.org/rdf/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

 a fhir:Parameters ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "FindSubjectMolecConseqOutput"] ; # 
  fhir:parameter ( [
fhir:name [ fhir:v "consequence" ] ;
    ( fhir:Parameters.parameter.resource [
a fhir:Observation ;
fhir:id [ fhir:v "MC1" ] ;
fhir:meta [
        ( fhir:profile [
fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence>         ] )       ] ;
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\">NM_001395525.1:c.-281+2T>C - intronic_variant:loss_of_function_variant</div>"       ] ;
fhir:status [ fhir:v "final" ] ;
      ( fhir:category [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
fhir:code [ fhir:v "laboratory" ]         ] )       ] [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GE" ]         ] )       ] ) ;
fhir:code [
        ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "molecular-consequence" ]         ] )       ] ;
fhir:subject [
fhir:reference [ fhir:v "Patient/HG00403" ]       ] ;
fhir:effective [ fhir:v "2023-04-01"^^xsd:date ] ;
      ( fhir:performer [
fhir:reference [ fhir:v "Organization/ExampleOrg" ]       ] ) ;
      ( fhir:interpretation [
        ( fhir:coding [
fhir:system [ fhir:v "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction"^^xsd:anyURI ] ;
fhir:code [ fhir:v "HIGH" ] ;
fhir:display [ fhir:v "High" ]         ] )       ] ) ;
      ( fhir:derivedFrom [
fhir:reference [ fhir:v "Observation/variantExampleMC" ]       ] ) ;
      ( fhir:component [
fhir:code [
          ( fhir:coding [
a loinc:51958-7 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "51958-7" ] ;
fhir:display [ fhir:v "Transcript reference sequence [ID]" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NM_001395525.1" ] ;
fhir:display [ fhir:v "NM_001395525.1" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "feature-consequence" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001575" ] ;
fhir:display [ fhir:v "splice_donor_variant" ]           ] [
fhir:system [ fhir:v "http://sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001627" ] ;
fhir:display [ fhir:v "intron_variant" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "functional-effect" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO_0002054" ] ;
fhir:display [ fhir:v "loss_of_function_variant" ]           ] )         ]       ] )     ] )
  ] [
fhir:name [ fhir:v "consequence" ] ;
    ( fhir:Parameters.parameter.resource [
a fhir:Observation ;
fhir:id [ fhir:v "MC2" ] ;
fhir:meta [
        ( fhir:profile [
fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence>         ] )       ] ;
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\">NM_001366781.1:c.90T>C - synonymous_variant</div>"       ] ;
fhir:status [ fhir:v "final" ] ;
      ( fhir:category [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
fhir:code [ fhir:v "laboratory" ]         ] )       ] [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GE" ]         ] )       ] ) ;
fhir:code [
        ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "molecular-consequence" ]         ] )       ] ;
fhir:subject [
fhir:reference [ fhir:v "Patient/HG00403" ]       ] ;
fhir:effective [ fhir:v "2023-04-01"^^xsd:date ] ;
      ( fhir:performer [
fhir:reference [ fhir:v "Organization/ExampleOrg" ]       ] ) ;
      ( fhir:interpretation [
        ( fhir:coding [
fhir:system [ fhir:v "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LOW" ] ;
fhir:display [ fhir:v "Low" ]         ] )       ] ) ;
      ( fhir:derivedFrom [
fhir:reference [ fhir:v "Observation/variantExampleMC" ]       ] ) ;
      ( fhir:component [
fhir:code [
          ( fhir:coding [
a loinc:48004-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48004-6" ]           ] ) ;
fhir:text [ fhir:v "coding HGVS" ]         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NM_001366781.1:c.90T>C" ] ;
fhir:display [ fhir:v "NM_001366781.1:c.90T>C" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:51958-7 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "51958-7" ] ;
fhir:display [ fhir:v "Transcript reference sequence [ID]" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NM_001366781.1" ] ;
fhir:display [ fhir:v "NM_001366781.1" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "feature-consequence" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001819" ] ;
fhir:display [ fhir:v "synonymous_variant" ]           ] )         ]       ] )     ] )
  ] [
fhir:name [ fhir:v "consequence" ] ;
    ( fhir:Parameters.parameter.resource [
a fhir:Observation ;
fhir:id [ fhir:v "MC3" ] ;
fhir:meta [
        ( fhir:profile [
fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence>         ] )       ] ;
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\">Molecular Consequence</div>"       ] ;
fhir:status [ fhir:v "final" ] ;
      ( fhir:category [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
fhir:code [ fhir:v "laboratory" ]         ] )       ] [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GE" ]         ] )       ] ) ;
fhir:code [
        ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "molecular-consequence" ]         ] )       ] ;
fhir:subject [
fhir:reference [ fhir:v "Patient/HG00403" ]       ] ;
fhir:effective [ fhir:v "2023-04-01"^^xsd:date ] ;
      ( fhir:performer [
fhir:reference [ fhir:v "Organization/ExampleOrg" ]       ] ) ;
      ( fhir:interpretation [
        ( fhir:coding [
fhir:system [ fhir:v "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction"^^xsd:anyURI ] ;
fhir:code [ fhir:v "MOD" ] ;
fhir:display [ fhir:v "Modifier" ]         ] )       ] ) ;
      ( fhir:derivedFrom [
fhir:reference [ fhir:v "Observation/variantExampleMC" ]       ] ) ;
      ( fhir:component [
fhir:code [
          ( fhir:coding [
a loinc:48004-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48004-6" ]           ] ) ;
fhir:text [ fhir:v "coding HGVS" ]         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NM_001395543.1:c.-171T>C" ] ;
fhir:display [ fhir:v "NM_001395543.1:c.-171T>C" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:51958-7 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "51958-7" ] ;
fhir:display [ fhir:v "Transcript reference sequence [ID]" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NM_001395543.1" ] ;
fhir:display [ fhir:v "NM_001395543.1" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "feature-consequence" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001623" ] ;
fhir:display [ fhir:v "5_prime_UTR_variant" ]           ] )         ]       ] )     ] )
  ] [
fhir:name [ fhir:v "consequence" ] ;
    ( fhir:Parameters.parameter.resource [
a fhir:Observation ;
fhir:id [ fhir:v "MC4" ] ;
fhir:meta [
        ( fhir:profile [
fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence>         ] )       ] ;
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\">Molecular Consequence</div>"       ] ;
fhir:status [ fhir:v "final" ] ;
      ( fhir:category [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
fhir:code [ fhir:v "laboratory" ]         ] )       ] [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GE" ]         ] )       ] ) ;
fhir:code [
        ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "molecular-consequence" ]         ] )       ] ;
fhir:subject [
fhir:reference [ fhir:v "Patient/HG00403" ]       ] ;
fhir:effective [ fhir:v "2023-04-01"^^xsd:date ] ;
      ( fhir:performer [
fhir:reference [ fhir:v "Organization/ExampleOrg" ]       ] ) ;
      ( fhir:interpretation [
        ( fhir:coding [
fhir:system [ fhir:v "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction"^^xsd:anyURI ] ;
fhir:code [ fhir:v "MOD" ] ;
fhir:display [ fhir:v "Modifier" ]         ] )       ] ) ;
      ( fhir:derivedFrom [
fhir:reference [ fhir:v "Observation/variantExampleMC" ]       ] ) ;
      ( fhir:component [
fhir:code [
          ( fhir:coding [
a loinc:51958-7 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "51958-7" ] ;
fhir:display [ fhir:v "Transcript reference sequence [ID]" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NM_001395544.1" ] ;
fhir:display [ fhir:v "NM_001395544.1" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "feature-consequence" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001627" ] ;
fhir:display [ fhir:v "intron_variant" ]           ] )         ]       ] )     ] )
  ] [
fhir:name [ fhir:v "variant" ] ;
    ( fhir:Parameters.parameter.resource [
a fhir:Observation ;
fhir:id [ fhir:v "variantExampleMC" ] ;
fhir:meta [
        ( fhir:profile [
fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant>         ] )       ] ;
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\">Variant</div>"       ] ;
fhir:status [ fhir:v "final" ] ;
      ( fhir:category [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
fhir:code [ fhir:v "laboratory" ]         ] )       ] [
        ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GE" ]         ] )       ] ) ;
fhir:code [
        ( fhir:coding [
a loinc:69548-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "69548-6" ] ;
fhir:display [ fhir:v "Genetic variant assessment" ]         ] )       ] ;
fhir:subject [
fhir:reference [ fhir:v "Patient/HG00403" ]       ] ;
fhir:effective [ fhir:v "2023-04-01"^^xsd:date ] ;
      ( fhir:performer [
fhir:reference [ fhir:v "Organization/ExampleOrg" ]       ] ) ;
fhir:value [
a fhir:CodeableConcept ;
        ( fhir:coding [
a loinc:LA9633-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA9633-4" ] ;
fhir:display [ fhir:v "Present" ]         ] )       ] ;
      ( fhir:component [
fhir:code [
          ( fhir:coding [
a loinc:48002-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48002-0" ] ;
fhir:display [ fhir:v "Genomic source class" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
a loinc:LA6683-2 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA6683-2" ] ;
fhir:display [ fhir:v "Germline" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:48013-7 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48013-7" ] ;
fhir:display [ fhir:v "Genomic reference sequence ID" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NC_000001.10" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:53034-5 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "53034-5" ] ;
fhir:display [ fhir:v "Allelic state" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
a loinc:LA6706-1 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA6706-1" ] ;
fhir:display [ fhir:v "Heterozygous" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:81252-9 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "81252-9" ] ;
fhir:display [ fhir:v "Discrete genetic variant" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NC_000001.10:g.86852621A>G" ] ;
fhir:display [ fhir:v "NC_000001.10:g.86852621A>G" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:81258-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "81258-6" ] ;
fhir:display [ fhir:v "Sample VAF" ]           ] )         ] ;
fhir:value [
a fhir:Quantity ;
fhir:value [ fhir:v "0.6"^^xsd:decimal ] ;
fhir:unit [ fhir:v "relative frequency of a particular allele in the specimen" ] ;
fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "1" ]         ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:69547-8 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "69547-8" ] ;
fhir:display [ fhir:v "Genomic Ref allele [ID]" ]           ] )         ] ;
fhir:value [ fhir:v "A" ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:69551-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "69551-0" ] ;
fhir:display [ fhir:v "Genomic Alt allele [ID]" ]           ] )         ] ;
fhir:value [ fhir:v "G" ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:92822-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "92822-6" ] ;
fhir:display [ fhir:v "Genomic coord system" ]           ] )         ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
a loinc:LA30100-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA30100-4" ] ;
fhir:display [ fhir:v "0-based interval counting" ]           ] )         ]       ] [
fhir:code [
          ( fhir:coding [
a loinc:81254-5 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "81254-5" ] ;
fhir:display [ fhir:v "Genomic allele start-end" ]           ] )         ] ;
fhir:value [
a fhir:Range ;
fhir:low [
fhir:value [ fhir:v "86852620"^^xsd:decimal ]           ]         ]       ] )     ] )
  ] ) . #