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Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative | Compartments: No defined compartments |
ShEx statement for moleculardefinition
PREFIX fhir: <http://hl7.org/fhir/> PREFIX fhirvs: <http://hl7.org/fhir/ValueSet/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> IMPORT <code.shex> IMPORT <Range.shex> IMPORT <string.shex> IMPORT <integer.shex> IMPORT <boolean.shex> IMPORT <Quantity.shex> IMPORT <markdown.shex> IMPORT <Reference.shex> IMPORT <Identifier.shex> IMPORT <Attachment.shex> IMPORT <DomainResource.shex> IMPORT <BackboneElement.shex> IMPORT <CodeableConcept.shex> start=@<MolecularDefinition> AND {fhir:nodeRole [fhir:treeRoot]} # Representation of a molecular definition <MolecularDefinition> EXTENDS @<DomainResource> CLOSED { a [fhir:MolecularDefinition]?;fhir:nodeRole [fhir:treeRoot]?; fhir:identifier @<OneOrMore_Identifier>?; # Unique ID for this particular # resource fhir:type @<code> AND {fhir:v @fhirvs:sequence-type}?; # aa | dna | rna fhir:location @<OneOrMore_MolecularDefinition.location>?; # Location of this molecule fhir:memberState @<OneOrMore_Reference_MolecularDefinition>?; # Member fhir:representation @<OneOrMore_MolecularDefinition.representation>?; # Representation } # Representation <MolecularDefinition.representation> EXTENDS @<BackboneElement> CLOSED { fhir:focus @<CodeableConcept>?; # The focus of the representation fhir:code @<OneOrMore_CodeableConcept>?; # A code of the representation fhir:literal @<MolecularDefinition.representation.literal>?; # A literal representation fhir:resolvable @<Attachment>?; # A resolvable representation of a # molecule that optionally contains # formatting in addition to the # specification of the primary # sequence itself fhir:extracted @<MolecularDefinition.representation.extracted>?; # A Molecular Sequence that is # represented as an extracted # portion of a different Molecular # Sequence fhir:repeated @<MolecularDefinition.representation.repeated>?; # A Molecular Sequence that is # represented as a repeated sequence # motif fhir:concatenated @<MolecularDefinition.representation.concatenated>?; # A Molecular Sequence that is # represented as an ordered # concatenation of two or more # Molecular Sequences fhir:relative @<MolecularDefinition.representation.relative>?; # A Molecular Definition that is # represented as an ordered series # of edits on a specified starting # sequence } # Coordinate Interval for this location <MolecularDefinition.location.sequenceLocation.coordinateInterval> EXTENDS @<BackboneElement> CLOSED { fhir:numberingSystem @<CodeableConcept>?; # Coordinate System fhir:start @<Quantity> OR @<Range> ?; # Start fhir:end @<Quantity> OR @<Range> ?; # End } # Location in context of a feature <MolecularDefinition.location.featureLocation> EXTENDS @<BackboneElement> CLOSED { fhir:geneId @<OneOrMore_CodeableConcept>?; # Gene Id } # A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence <MolecularDefinition.representation.extracted> EXTENDS @<BackboneElement> CLOSED { fhir:startingMolecule @<Reference> AND {fhir:link @<MolecularDefinition> ? }; # The Molecular Sequence that serves # as the parent sequence, from which # the intended sequence will be # extracted fhir:start @<integer>; # The start coordinate (on the # parent sequence) of the interval # that defines the subsequence to be # extracted fhir:end @<integer>; # The end coordinate (on the parent # sequence) of the interval that # defines the subsequence to be # extracted fhir:coordinateSystem @<CodeableConcept>; # The coordinate system used to # define the interval that defines # the subsequence to be extracted. # Coordinate systems are usually 0- # or 1-based fhir:reverseComplement @<boolean>?; # A flag that indicates whether the # extracted sequence should be # reverse complemented } # A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence <MolecularDefinition.representation.relative> EXTENDS @<BackboneElement> CLOSED { fhir:startingMolecule @<Reference> AND {fhir:link @<MolecularDefinition> ? }; # The Molecular Sequence that serves # as the starting sequence, on which # edits will be applied fhir:edit @<OneOrMore_MolecularDefinition.representation.relative.edit>?; # An edit (change) made to a sequence } # Location of this molecule in context of a sequence <MolecularDefinition.location.sequenceLocation> EXTENDS @<BackboneElement> CLOSED { fhir:sequenceContext @<Reference> AND {fhir:link @<MolecularDefinition> ? }; # Reference sequence fhir:coordinateInterval @<MolecularDefinition.location.sequenceLocation.coordinateInterval>?; # Coordinate Interval for this # location fhir:strand @<CodeableConcept>?; # Forward or Reverse } # Cytoband Interval <MolecularDefinition.location.cytobandLocation.cytobandInterval> EXTENDS @<BackboneElement> CLOSED { fhir:chromosome @<CodeableConcept>; # Chromosome fhir:startCytoband @<MolecularDefinition.location.cytobandLocation.cytobandInterval.startCytoband>?; # Start fhir:endCytoband @<MolecularDefinition.location.cytobandLocation.cytobandInterval.endCytoband>?; # End } # One element of a concatenated Molecular Sequence <MolecularDefinition.representation.concatenated.sequenceElement> EXTENDS @<BackboneElement> CLOSED { fhir:sequence @<Reference> AND {fhir:link @<MolecularDefinition> ? }; # The Molecular Sequence # corresponding to this element fhir:ordinalIndex @<integer>; # The ordinal position of this # sequence element within the # concatenated Molecular Sequence } # Location of this molecule <MolecularDefinition.location> EXTENDS @<BackboneElement> CLOSED { fhir:sequenceLocation @<MolecularDefinition.location.sequenceLocation>?; # Location of this molecule in # context of a sequence fhir:cytobandLocation @<MolecularDefinition.location.cytobandLocation>?; # Location of this molecule in # context of a cytoband fhir:featureLocation @<OneOrMore_MolecularDefinition.location.featureLocation>?; # Location in context of a feature } # Start <MolecularDefinition.location.cytobandLocation.cytobandInterval.startCytoband> EXTENDS @<BackboneElement> CLOSED { fhir:arm @<code> OR @<string> ?; # Arm fhir:region @<code> OR @<string> ?; # Region fhir:band @<code> OR @<string> ?; # Band fhir:subBand @<code> OR @<string> ?; # Sub-band } # A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences <MolecularDefinition.representation.concatenated> EXTENDS @<BackboneElement> CLOSED { fhir:sequenceElement @<OneOrMore_MolecularDefinition.representation.concatenated.sequenceElement>; # One element of a concatenated # Molecular Sequence } # A literal representation <MolecularDefinition.representation.literal> EXTENDS @<BackboneElement> CLOSED { fhir:encoding @<CodeableConcept>?; # The encoding used for the # expression of the primary sequence fhir:value @<string>; # The primary (linear) sequence, # expressed as a literal string } # An edit (change) made to a sequence <MolecularDefinition.representation.relative.edit> EXTENDS @<BackboneElement> CLOSED { fhir:editOrder @<integer>?; # The order of this edit, relative # to other edits on the starting # sequence fhir:coordinateSystem @<CodeableConcept>; # The coordinate system used to # define the edited intervals on the # starting sequence. Coordinate # systems are usually 0- or 1-based fhir:start @<integer>; # The start coordinate of the # interval that will be edited fhir:end @<integer>; # The end coordinate of the interval # that will be edited fhir:replacementMolecule @<Reference> AND {fhir:link @<MolecularDefinition> ? }; # The sequence that defines the # replacement sequence used in the # edit operation fhir:replacedMolecule @<Reference> AND {fhir:link @<MolecularDefinition> ? }?; # The sequence on the 'starting' # sequence for the edit operation, # defined by the specified interval, # that will be replaced during the # edit } # Reference Genome <MolecularDefinition.location.cytobandLocation.genomeAssembly> EXTENDS @<BackboneElement> CLOSED { fhir:organism @<CodeableConcept>?; # Species of the organism fhir:build @<CodeableConcept>?; # Build number fhir:accession @<CodeableConcept>?; # Accession fhir:description @<markdown> OR @<string> ?; # Genome assemble description } # End <MolecularDefinition.location.cytobandLocation.cytobandInterval.endCytoband> EXTENDS @<BackboneElement> CLOSED { fhir:arm @<code> OR @<string> ?; # Arm fhir:region @<code> OR @<string> ?; # Region fhir:band @<code> OR @<string> ?; # Band fhir:subBand @<code> OR @<string> ?; # SuBand } # Location of this molecule in context of a cytoband <MolecularDefinition.location.cytobandLocation> EXTENDS @<BackboneElement> CLOSED { fhir:genomeAssembly @<MolecularDefinition.location.cytobandLocation.genomeAssembly>; # Reference Genome fhir:cytobandInterval @<MolecularDefinition.location.cytobandLocation.cytobandInterval>; # Cytoband Interval } # A Molecular Sequence that is represented as a repeated sequence motif <MolecularDefinition.representation.repeated> EXTENDS @<BackboneElement> CLOSED { fhir:sequenceMotif @<Reference> AND {fhir:link @<MolecularDefinition> ? }; # The sequence that defines the # repeated motif fhir:copyCount @<integer>; # The number of repeats (copies) of # the sequence motif } #---------------------- Cardinality Types (OneOrMore) ------------------- <OneOrMore_Identifier> CLOSED { rdf:first @<Identifier> ; rdf:rest [rdf:nil] OR @<OneOrMore_Identifier> } <OneOrMore_MolecularDefinition.location> CLOSED { rdf:first @<MolecularDefinition.location> ; rdf:rest [rdf:nil] OR @<OneOrMore_MolecularDefinition.location> } <OneOrMore_Reference_MolecularDefinition> CLOSED { rdf:first @<Reference> AND {fhir:link @<MolecularDefinition> } ; rdf:rest [rdf:nil] OR @<OneOrMore_Reference_MolecularDefinition> } <OneOrMore_MolecularDefinition.representation> CLOSED { rdf:first @<MolecularDefinition.representation> ; rdf:rest [rdf:nil] OR @<OneOrMore_MolecularDefinition.representation> } <OneOrMore_CodeableConcept> CLOSED { rdf:first @<CodeableConcept> ; rdf:rest [rdf:nil] OR @<OneOrMore_CodeableConcept> } <OneOrMore_MolecularDefinition.representation.relative.edit> CLOSED { rdf:first @<MolecularDefinition.representation.relative.edit> ; rdf:rest [rdf:nil] OR @<OneOrMore_MolecularDefinition.representation.relative.edit> } <OneOrMore_MolecularDefinition.location.featureLocation> CLOSED { rdf:first @<MolecularDefinition.location.featureLocation> ; rdf:rest [rdf:nil] OR @<OneOrMore_MolecularDefinition.location.featureLocation> } <OneOrMore_MolecularDefinition.representation.concatenated.sequenceElement> CLOSED { rdf:first @<MolecularDefinition.representation.concatenated.sequenceElement> ; rdf:rest [rdf:nil] OR @<OneOrMore_MolecularDefinition.representation.concatenated.sequenceElement> } #---------------------- Value Sets ------------------------ # Type if a sequence -- DNA, RNA, or amino acid sequence. fhirvs:sequence-type ["aa" "dna" "rna"]
Usage note: every effort has been made to ensure that the ShEx files are correct and useful, but they are not a normative part of the specification.
FHIR ®© HL7.org 2011+. FHIR R6 hl7.fhir.core#6.0.0-ballot2 generated on Mon, Nov 11, 2024 05:58+0000.
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