MolecularDefinition.shex

PREFIX fhir: <http://hl7.org/fhir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX loinc: <https://loinc.org/rdf/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX Map: <http://shex.io/extensions/Map/#>
PREFIX metab: <http://a.example/->

start=<#MolecularDefinition>

<#MolecularDefinition> CLOSED {
  a [fhir:MolecularDefinition] ;
  fhir:nodeRole [fhir:treeRoot] ;
  fhir:id { fhir:v xsd:string } ; # "example-allelesliced1"
  fhir:moleculeType { fhir:coding @<#OneOrMore_MolecularTypeCoding> } ;
  fhir:location @<#OneOrMore_Location> ; # 
  fhir:representation @<#OneOrMore_Representation> #
}

<#OneOrMore_MolecularTypeCoding> CLOSED {
  rdf:first @<#MolecularTypeCoding> ;
  rdf:rest [rdf:nil] OR @<#OneOrMore_MolecularTypeCoding>
}

<#MolecularTypeCoding> CLOSED {
  fhir:system { fhir:v xsd:anyURI } ; # "http://hl7.org/fhir/sequence-type"
  fhir:code { fhir:v xsd:string } ; # "dna"
  fhir:display { fhir:v xsd:string } # "DNA Sequence"
}

<#OneOrMore_Location> CLOSED {
  rdf:first @<#Location> ;
  rdf:rest [rdf:nil] OR @<#OneOrMore_Location>
}

<#Location> CLOSED {
  fhir:sequenceLocation CLOSED {
    fhir:sequenceContext CLOSED {
      fhir:link IRI ; # <http://hl7.org/fhir/MolecularDefinition/example-sequence-lrg584>
      fhir:reference { fhir:v xsd:string } ; # "MolecularDefinition/example-sequence-lrg584"
      fhir:type { fhir:v xsd:anyURI } ; # "MolecularDefinition"
      fhir:display { fhir:v xsd:string } # "Starting Sequence Resource: LRG_584"
    } ;
    fhir:coordinateInterval CLOSED {
      fhir:coordinateSystem CLOSED {
        fhir:system CLOSED {
          fhir:coding @<#OneOrMore_LocationIntervalCoordinateSystemCoding> ;
          fhir:text { fhir:v xsd:string } # "0-based interval counting"
        }
      } ;
      fhir:start CLOSED {
        a [fhir:Quantity] ;
        fhir:value { fhir:v xsd:decimal } # "5001"
      } ;
      fhir:end CLOSED {
        a [fhir:Quantity] ;
        fhir:value { fhir:v xsd:decimal } # "97867"
      }
    }
  }
}

<#OneOrMore_LocationIntervalCoordinateSystemCoding> CLOSED {
  rdf:first @<#LocationIntervalCoordinateSystemCoding> ;
  rdf:rest [rdf:nil] OR @<#OneOrMore_LocationIntervalCoordinateSystemCoding>
}

<#LocationIntervalCoordinateSystemCoding> CLOSED {
  a [loinc:~] ; # LA30100-4
  fhir:system { fhir:v xsd:anyURI %Map:{ metab:locCoordSystemSystem %} } ; # "http://loinc.org"
  fhir:code { fhir:v xsd:string %Map:{ metab:locCoordSystemCode %} } ; # "LA30100-4"
  fhir:display { fhir:v xsd:string %Map:{ metab:locCoordSystemDisp %} } # "0-based interval counting"
}

<#OneOrMore_Representation> CLOSED {
  rdf:first @<#Representation> ;
  rdf:rest [rdf:nil] OR @<#OneOrMore_Representation>
}

<#Representation> CLOSED {
  fhir:focus CLOSED {
    fhir:coding @<#OneOrMore_RepresentationFocusCoding>
  } ;
  fhir:resolvable CLOSED {
    fhir:link IRI ; # <http://hl7.org/fhir/DocumentReference/example-genomicFile-ng0083843>
    fhir:reference { fhir:v xsd:string } # "DocumentReference/example-genomicFile-ng0083843"
  } ? ;
  fhir:relative CLOSED {
    fhir:startingMolecule CLOSED {
      fhir:link IRI ; # <http://hl7.org/fhir/MolecularDefinition/example-sequence-lrg584>
      fhir:reference { fhir:v xsd:string } ; # "MolecularDefinition/example-sequence-lrg584"
      fhir:type { fhir:v xsd:anyURI } ; # "MolecularDefinition"
      fhir:display { fhir:v xsd:string } # "Starting Sequence Resource: LRG_584"
    } ;
    fhir:edit @<#OneOrMore_RelativeEdit>
  } ?
}

<#OneOrMore_RepresentationFocusCoding> CLOSED {
  rdf:first @<#RepresentationFocusCoding> ;
  rdf:rest [rdf:nil] OR @<#OneOrMore_RepresentationFocusCoding>
}

<#RepresentationFocusCoding> CLOSED {
  fhir:code { fhir:v xsd:string } ; # "allele-state", "context-state"
  fhir:display { fhir:v xsd:string } # "Allele State", "Context State"
}

<#OneOrMore_RelativeEdit> CLOSED {
  rdf:first @<#RelativeEdit> ;
  rdf:rest [rdf:nil] OR @<#OneOrMore_RelativeEdit>
}

<#RelativeEdit> CLOSED {
  fhir:coordinateInterval CLOSED {
    fhir:coordinateSystem CLOSED {
      fhir:system CLOSED {
        fhir:coding @<#OneOrMore_RelativeEditIntervalCoordinateSystemCoding> ;
        fhir:text { fhir:v xsd:string } # "0-based interval counting"
      }
    }
  } ;
  fhir:replacementMolecule CLOSED {
    fhir:link IRI ; # <http://hl7.org/fhir/MolecularDefinition/example-sequence-t>
    fhir:reference { fhir:v xsd:string } ; # "MolecularDefinition/example-sequence-t"
    fhir:type { fhir:v xsd:anyURI } ; # "MolecularDefinition"
    fhir:display { fhir:v xsd:string } # "Replacement Sequence Resource: T"
  } ;
  fhir:replacedMolecule CLOSED {
    fhir:link IRI ; # <http://hl7.org/fhir/MolecularDefinition/example-sequence-c>
    fhir:reference { fhir:v xsd:string } ; # "MolecularDefinition/example-sequence-c"
    fhir:type { fhir:v xsd:anyURI } ; # "MolecularDefinition"
    fhir:display { fhir:v xsd:string } # "Replaced Sequence Resource: C"
  }
}

<#OneOrMore_RelativeEditIntervalCoordinateSystemCoding> CLOSED {
  rdf:first @<#RelativeEditIntervalCoordinateSystemCoding> ;
  rdf:rest [rdf:nil] OR @<#OneOrMore_RelativeEditIntervalCoordinateSystemCoding>
}

<#RelativeEditIntervalCoordinateSystemCoding> CLOSED {
  a [loinc:~] ; # LA30100-4
  fhir:system { fhir:v xsd:anyURI } ; # "http://loinc.org"
  fhir:code { fhir:v xsd:string } ; # "LA30100-4"
  fhir:display { fhir:v xsd:string } # "0-based interval counting"
}